Got my low idle issue fixed!
This issue was caused by me after balancing the throttle bodies for the first time. Got them balanced but anytime I came to a stop the idle would go way low (like around 800 rpm) for a little while then eventually rise back to what it was supposed to be (1170 rpm). Very occasionally it would stall if the throttle was quickly opened then closed.
So today I had time to pull the tank & airbox and try out my theory. Hooked up the computer to get the throttle balance readout. #1 was around 63, #2 and #3 around 62 and it was indicating balanced. However the air screw for #1 was out 1.5 turns, #2 and #3 were only out 1/2 turn. I theorized that it was just not getting enough idle air bypass thru 2 and 3 thus causing the low idle.
So first I unscrewed 2 & 3 to also be 1.5 turns out, then fired it up with the computer hooked up. Was now showing unbalanced with #1 about 64, #2 & #3 about 59. Unscrewed #1 another full turn to bring it down to about 60 and got "balanced" on the screen. So now all 3 are in the vicinity of 59-60, #1 is 2.5 turns out, #2 and #3 are 1.5 turns out. Seemed to be running very smooth so I bolted the tank down, put the seat back on and took a ride around without the airbox or plastics to check it out. BTW it sounds great riding around without the airbox!
Sure enough, smooth as silk and no more low idle! Acts just like it used to act before I fucked with it back at the 12K service.
So I guess my theory was correct and now with 2 & 3 opened up a bit more it's got enough air bypassing the throttle plate to return to proper idle when the throttle is closed.
So now I've finally got it right: balanced throttles and proper driveability. Now you can all learn from my mistakes.