Thanks for the advice above. I figured that I needed to be a bit more patient with it and that taking the pinion post out would create too much unnecessary work. Glad to hear it from someone else!
Now I need another opinion that stems from doing some searching and not finding enough information;
I bought my bike used with 3300 miles on it from an outwardly proud "Christian Firefighter" in Virginia, who said it was in perfect shape other than the right side number plate being damaged from a soft-bag pressing it against the muffler. We already know where this is going, right? After riding it a few times I noticed that the only time my oil was clean was when I bought it and trailered it 8 hours home. The oil must have just been freshly changed the day I looked at it and bought it..
I thought it had a knocking noise when I was looking at it however it was probably just the standard noise bouncing off the skidplate that I had read about... nothing too serious because the oil was clean and the bike seemed to be running well and otherwise sounded normal. I initially cycled oil through it after every few hundred miles (just for my peace of mind) and noticed that the oil would never stay clean for more than one or two trips around the block. It would turn a cloudy black color. I called this guy to ask him what he knew and of course he wouldn't reply. Then I took it to two local dealers who had no idea what it could be, wanted me to leave it with them, and charge me an exorbitant amount of money to fix something that I could probably figure out myself.
I did my research and cracked the case to look for the famous Primary Drive Gear Nut issue. Lo-and-behold! It was about 3 to 4 threads loose from where it should be tightened at. It was machining off the corner of the clutch basket. I've used a magnetic oil plug, which would present small amounts of shavings, however nothing that looked too serious. When I pulled the case off there was a little cranny in the case behind the gasket that trapped enough metal to fill a pen cap, probably more aluminum than anything. The nut which is made of stronger metal didn't have much damage. I figure that's the reason that I didn't get many flakes on my oil plug. By this time, I'm kicking myself for not trusting my instinct with the knocking noise and cursing this righteous "Christian Firefighter's" name up and down.
Bottom line, I have to live with the issue, chalk it up as experience, and probably rebuild or buy a new motor sometime down the road. I would love to have more faith in mankind, however these kind of circumstances make it difficult.
MY CURRENT QUESTION
Considering that the bike now has about 5500 miles on it. I changed the oil wayyyy more than I should have. I cleaned the surfaces and put red locktight on the Primary Drive Gear Nut and torqued it. The NSU was already tight so I put locktight on it and tightened it back up. Hopefully the oil will stay clean after I cycle it once more.
What could be the next domino(s) to fall as a result of putting mileage on the engine with metal shavings floating around for a few thousand miles?
What kind of engine life would you guys think that I'll have? I ride pretty conservative and sometimes get a bit spirited.
Is there anything else that I should be wary of?
Once again, I appreciate any advice and I hope this helps others as well.