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Old 03-31-2013, 09:22 PM   #1
AdvX OP
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'06 Hammer - Mysterious Hiccups

I've been trying to troubleshoot an issue with my 2006 R1200GS (~56k mi) off and on for months. Does anyone have any ideas?

Symptoms:
- at idle, when I quickly rev the engine, the engine appears to slightly hesitate as it works its way up the tachometer, and I can hear the silencer baffles working to suppress backfire.
- at speed, I can sometimes accelerate quickly in 1st gear, but running the throttle up quickly in 2nd - 6th produces the same symptoms as at idle, only more pronounced. The engine often will not exceed ~4000-5000 RPM and will only 'hiccup'. It acts as if it's hitting the governor at RPM redline, only at much lower RPMs. I've found I can delay the hiccup onset if I accelerate slowly and smoothly. I'm able to roll the throttle on much quicker without symptoms in 1st gear.
- the symptoms include multiple attempts to 'back-fire'
- noticed my MPG is 5-10 less than normal
- symptoms appear to be independent of speed and throttle position

What I've done so far:
- checked the air filter and airways up to the airbox for proper flow. I even removed the filter and reved a few times - same symptoms.
- checked the air and fuel hoses for kinks or tears. Nothing, and they've been triple checked at this point.
- fuel pump filter - it's clean.
- LOOKED at the injectors - appear very clean (made sure not to adjust their positioning)
- replaced the fuel pressure manifold. I thought the internal diaphragm might be sticking and causing the hiccups. New OEM pressure manifold, but same symptoms.


Does anyone have any ideas?

Does anyone know if the governor setting can creep? The only time I've experienced similar symptoms is when I've hit the RPM redline (hasn't happened often), although I don't think I remember the silencer baffles exercising so much when I hit redline.


I'd appreciate any help - I'm itching to take advantage of this warm Northern Utah weather.

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Old 04-01-2013, 12:20 AM   #2
Japanviking
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Maybe a problem with the secondary plugs?
have you checked all the connectors for the spark plugs?

I would take them apart and clean them. maybe take the plugs out and see how they look.
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Old 04-01-2013, 04:06 AM   #3
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Coils.

Check my thread from last summer, you'll see all the answers I think.
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Old 04-01-2013, 05:14 AM   #4
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Yep! Coils!

I had the same type problems recently on my '07. Mine was the right primary coil.
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Old 04-01-2013, 04:59 PM   #5
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Mine did the same thing, it was the electrical connection to the fuel pump controller on top-outside of the fuel pump flange, the connection was loose from a prior service. Could be this or the fuel pump controller itself.
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Old 04-01-2013, 07:23 PM   #6
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JapanViking - I haven't checked primary or secondary plugs since I replaced them at 30K with NKG Iridiums. I'll do a visual check and run a few tests.

SR1 & Goldberg - I read SR1's 'GS cutting out' thread. Wish I would have stumbled across it a few months ago. I'm going to take a look at the plugs, then do a few of the coil tests described in that thread. Maybe I'll luck out and be able to isolate a bad plug, but I get the feeling it's a coil - most likely a primary. (Although I never experienced any of the jerking SR1 initially encountered.) Looks like I should be able to isolate it if that's the case, even if it's only intermittent.

Simoneau - I checked out the fuel pump connector and cleaned the connection when I removed it to check the pump screen. I didn't notice any looseness or corrosion, but I'll pay it another visit if the plugs or primary coils don't pan out. I also didn't look too closely at the controller connection. I'll check it out. I've been in 'limp' mode before, but this feels different. (I can still get past 90mph, but it takes much longer than usual.)


Thank you all for the ideas. I should be able to troubleshoot on Wednesday - will let you know how it goes.


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Old 04-01-2013, 08:28 PM   #7
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Check the plugs carefully, I had a hairline crack in the porcelain part on one of mine that caused similar symptoms.
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Old 04-04-2013, 08:44 PM   #8
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still troubleshooting - any more suggestions?

Ok, so here's what I did and how the bike responded:

First, I pulled the primary coil protectors off both sides. On the right, I noticed the primary coil had backed off the plug about 1/4 inch. I pushed it back on, then started the bike. At idle and after revving, the bike exhibited the same hiccupping.

Second, I started the bike and removed the left primary coil off the plug. I didn't notice the engine running any differently at idle or after revving (in neutral). I replaced the left primary, then removed the right primary (bike still running). I THOUGHT the bike stumbled a bit more than normal. After revving, it appeared to act a little rougher. I replaced the right primary, but didn't notice an improvement in engine performance - either or idle or at high RPM.

**here's the kicker - the bike has not reverted to it's previous symptoms - it now only runs like it initially did when I removed the right primary for the first time. Instead of hiccupping, now the bike just goes quiet when I rev quickly, like I didn't even move the throttle. Then, it engages quickly. When riding, I now experience the jerking SR1 described in his thread last summer.

Third, I turned off the ignition and removed both primary coils and inspected them closely. I didn't notice any cracks or other noticeable damage, but both have a little of the black coating rubbed off the metal housing near where it transitions to the rubber boot (which houses the plug). I wasn't sure if these rub marks would allow arcing to the magnesium, but I didn't see any witness marks in the engine cap tube where I would expect to see something.

Fourthly, I repeated step two, but the operation didn't change.

Fifthly, while the bike was running, I removed the left secondary coil connector from the coil. The engine immediately ran noticeably rougher at idle, which surprised me because I've read the secondary plugs don't engage until higher RPMs. At higher RPMs, the engine roughness was even more noticeable.

Sixthness, I replaced the right secondary connector and removed the left secondary coil connector. I immediately noticed the same symptoms as when I removed the left secondary coil connector. Upon reattaching the right connector, the engine operation immediately improved to the same symptoms that manifested after step 2 - both at idol and at fast revving.

Seventhly, I turned the ignition off and closely inspected both primary plugs. The plugs have about 25k miles on them, but they look relatively good for that mileage. There wasn't any sign of plug damage or abnormal engine operation.

Eighth through eleventh, I repeated steps 1-6 a few times, in various order, and was met with similar results. On one iteration, I even switched the left and right primary coils - no change to behavior. Hell, I even tried Poolside's Quantitative Tapping Method (QTM). No luck.

Lastly, I measured the resistance on the primary coils, not that I know what the resistance SHOULD be, but more to see if there was a significant difference between the two. They both measured 1.4 ohms (with a decent Fluke).

I rode the bike to work today (primary coils still switched), and I still experience the slightly different symptoms which materialized after step 2. When attempting to quickly accelerate, the engine acts like the throttle didn't even move, then occasionally jerks.


So, that's where I am. I'm now wondering of both primary coils are intermittent. I also realize that although I began my testing with a cold engine, it warmed up considerably during my testing. I still didn't notice any change in operation after Infamous Step 2. The bike had plenty of time to warm up on the trip in to work today, but still no noticeable difference.

I'm thinking of performing the same steps again, but beginning with a hot engine. I'm also thinking of peeking at the secondary plugs, but the troubleshooting doesn't seem to implicate the secondary plugs or coils. Could also replace the primary plugs, just in case.

I guess it could also be damage to my electrical harness where signals to the left primary coil are interrupted, but now I'm really grasping as I imagine that's pretty rare without a crash.


Does anyone have any other ideas?

thank you -
booger

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Old 04-05-2013, 02:59 AM   #9
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I still think it's a coil. And I still never quite figured how how I was supposed to identify "where" the problem was, though I tried hard to learn.

The bottom line is I have three extra coils. What do you think I did?
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Old 04-06-2013, 02:54 AM   #10
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Sir,

As it seems it is linked to the left side (no change in rpm's when disconnecting coil), may I suggest to change the primary spark plugs? Then see what happens when disconnecting the primary coils left and right. If right side is now not responding to the removal of the coil, the spark plug is suspect.
All in all, as mentioned above, the primary coils are also a suspect for me. Even both can be defective.
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Old 04-06-2013, 03:15 AM   #11
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Be careful with running the engine with plug caps disconnected. Doing so might damage the components.
With one extra spark plug you can connect it if you are pulling of the caps. You can also check that you have a spark by doing this.
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Old 04-06-2013, 04:02 AM   #12
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Sniff test

I'll certainly bow to the guys who have had a similar problem but will throw in my thoughts,,,,

Lower gas mileage = how does the exhaust smell? Can you detect it as rich and any unburnt fuel ?

Go back to basics and do the simple stuff first, check for spark, check the wiring, since the left coil disconnect made no difference that certainly seems to be the correct place to chase, and swapping coils made no difference so assuming both didn't go bad (not impossible but unlikely given your results) bark up that tree..

Swap left for right one item at a time where you can and the plug, plug wire etc back to a main branch will likely be your culprit. A few cheap good spares from the bone yard could come in handy.

Report back as you go
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Old 04-06-2013, 09:36 PM   #13
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Round 3 (R12GS leading 2-1)

Thanks to everyone for your ideas. Here's what I did today:

1. Drove the bike to NAPA to pick up new spark plugs - warmed up the engine for further troubleshooting.
--Same symptoms.

2. Engine is hot. Removed the left primary coil, inserted a new NGK iridium (single spark - same as the plugs I've been running for ~25k) into the coil, but left the old plug in the engine. So, the coil was hanging free with a new plug in it. Cranked the engine and ran thorough a few rev cycles.
--Same symptoms. When I rev quickly and freeze the throttle at the point the symptoms begin, I can keep the engine in this 'defibrillation' for a while, and I do smell unburned fuel when I keep it there.

3. Ignition - off. Reconnected left primary (old plug still installed in engine), and performed step 2 on the right side.
--Same symptoms.

4. Ignition - off. Disconnected left primary coil again and inserted new plug in the coil. Now both primary coils were hanging free with new plugs in them, and old plugs are still in the engine. Cranked the engine and ran through a few rev cycles.
--Same symptoms. I also noticed I was not getting ANY spark from the new plugs installed in the primary coils - even checked in a very dark environment. No detectable spark, but I only performed this check at idle.


At this point, I'm thinking a few things may be possible:
A. Both primary coils are bad.
B. The ECU has stopped sending fire signals to the primary coils (maybe I really have been in some sort of 'limp home' mode).
C. The ECU somehow knows when a coil is disconnected and responds by cutting the signals to the disconnected coil.
D. The circuit between the ECU and coils may be fuze protected, and if so, the fuzes may be blown.
E. I may have a bad connection between the harness and the coils, or between the coils and the spark plugs.


5. I didn't think it was the plugs at this point, but I replaced the primaries anyway with new NGK Iridium single spark plugs. Reconnected the primary coils, cranked the engine, and ran through a few rev cycles. I took a hard look inside the coils but didn't see anything strange. I also started paying much closer attention to pushing the coils completely onto the plugs - hearing/feeling the snap, the pushing a little harder just to be sure.
--Same symptoms.

6. I wanted to see if the primary coils were really receiving signals, but I don't have a good scope. My fluke does happen to have a small metering function which could help me see the short firing signals the engine control unit (ECU) sends to the coils. So I rigged a few test leads, disconnected the harness from the primary coils, and checked the voltages and currents coming through the harness from the ECU. I checked one at a time at the coil connector - right, then left, then repeated - right, left.
--I'm getting consistent voltage (~12 VDC range, if I remember correctly) and current (which jumps around on the Fluke as expected) from pins 1 and 3. (My 1.4 ohm primary coil resistance measurement in Round 2 was made between pins 1 and 3.) Both sides are relatively consistent here, but because I'm using a digital multimeter instead of a scope, I don't think the values (especially current) are that accurate. I noticed a little voltage fluctuation between pins 1 and 2 and also between 2 and 3 in my millivolt range, but no current. I expect this is normal since my wiring diagram shows all coil #2 pins are common - I'm probably just picking up noise from the ground line.


At this point, I'm even more convinced the primary coils are bad, even with how improbable this sounds. I don't see spark with new plugs, but the coils are receiving their firing commands and apparently adequate voltage.

What's troubling me is I'm surprised the bike is running as well as it is if only the secondary plugs are sparking. I just replaced the secondary plugs (had the TT bars and cylinder cap protectors off for an oil change anyway), and they look just as worn as the primary plugs. Also, none of the plugs had fouled electrodes - something I'd expect if they weren't sparking or were sparking weakly/intermittently.

What's also troubling is the bike is running the way I think it would if I had bad SECONDARY coils, not bad primary coils. Thinking through all the symptoms and what troubleshooting has revealed, I started thinking I MUST have confused the primary and secondary coils. Checked my Haynes (which isn't great), but no - the secondaries are below the block and the primaries connect through the cylinder caps, just like I remembered.


I'm planning on ordering two new primary coils unless someone can talk me down from this tree.

SR1 - I bet you ordered two new primary coils and two new secondary coils. Am I right? And you have three extra coils because you really only had one bad coil?

I think it's possible I only have one bad coil and completely overlooked something whilest troubleshooting the coils/plugs, but there are worse things than having an extra primary coil. Now, if I find myself with TWO extra primary coils, I may invent some new words. (SR1, maybe you already have a few reserved for such a situation?)


Again, thank you all for your input.
If I don't see a compelling rebuttal here in the next few days, I'll be ordering new primary coils.

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Old 04-07-2013, 04:34 AM   #14
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Quote:
Originally Posted by AdvX View Post
Now, if I find myself with TWO extra primary coils, I may invent some new words. (SR1, maybe you already have a few reserved for such a situation?)

The situation is cut and dry for some it seems, and many seemed to "know" the answer to my issue before I did. It seemed the problem moved or gave improper results based on the troubleshooting technique. I too thought the symptom only appeared when "secondaries" were supposed to be firing. Several people were adamant that secondaries don't fire in low RPMs. My bike will run and (poorly) accelerate with only the secondaries plugged in.

Bottom line, I got some confusing, weird results no matter what I unplugged. I ordered secondaries first, but no positive results. Ordered to primaries and tried each side. When I replaced the faulty one, it was like flipping a switch, PERFECT.

Despite all the pull-this-pull-that troubleshooting, it wound up being a "trial and error" and yes, it was pricey and infuriating.
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Old 04-27-2013, 11:57 PM   #15
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thanks everyone

The two primary coils finally came in - they were waiting for me when I returned from vacation.

I installed the left coil first, started the bike and immediately noticed the return of the original symptoms: rough running, delay during acceleration, but not the violent lurching that began after I started troubleshooting.

I powered down the bike and replaced the right primary coil. Started it up and . . . it runs fine, just like it should.

It appears I only began with one bad coil - probably the left, but my troubleshooting methods (or maybe just all of the coil connections/disconnections) likely damaged the right primary coil. Still, they were necessary to zero in on the primary failure mode. If I had it to do over again, I would have ensured the bike was off each time I disconnected an ignition coil, but I also don't know if that would have changed anything. Also, I would have read SR1's post on the issue earlier. Thanks, SR1.

It's possible the right coil was just on its way out, and the extra handling proved too much for it.

Thanks to everyone who offered advice. You saved me a lot of time and probably a lot of money.

Now I'm just looking forward to getting out there and riding the bike the way it was intended. Starting tomorrow.



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