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I presume that you are using Autolite sparkplugs. Oddly enough, they seem to help. I also presume that you have replaced the throttle cables.
The aftermarket exhaust is not helping. In theory it flows better, which means that upstream the mixture would tend to be leaner. If the O2 sensor is still installed then it can correct somewhat, but not entirely. If not, then all bets are off.
I suggest checking the Big Brass Screw (BBS) settings. They should be about 1 to 1 1/2 turns out from fully closed if the factory (and others) set things up properly. If they are substantially different, you should clean the throttle bodies and BBS ports thoroughly with carb cleaner and swabbing with Q-tips, and make the airflows equal by adjusting those do-not-touch throttle stop screws.
Assuming your throttle shafts are not worn (not likely at 12K miles), you should be able to get surge free operation after a anal intake valve settings, with the BBSs set out 1 1/2 turns each, slak the throttle cables, and then adjust the idle with the throttle stop screws, then adjust the TPS to .385 V, then adjust the throttle cables for equal pull open with a carb equalizer setup.
I think surging is caused by one cylinder dropping out at part throttle closed loop control. My R1100RT at 20K miles was terrible on surging til I did the above.
I suggest checking the Big Brass Screw (BBS) settings. They should be about 1 to 1 1/2 turns out from fully closed if the factory (and others) set things up properly. If they are substantially different, you should clean the throttle bodies and BBS ports thoroughly with carb cleaner and swabbing with Q-tips, and make the airflows equal by adjusting those do-not-touch throttle stop screws.
Assuming your throttle shafts are not worn (not likely at 12K miles), you should be able to get surge free operation after a anal intake valve settings, with the BBSs set out 1 1/2 turns each, slak the throttle cables, and then adjust the idle with the throttle stop screws, then adjust the TPS to .385 V, then adjust the throttle cables for equal pull open with a carb equalizer setup.
I think surging is caused by one cylinder dropping out at part throttle closed loop control. My R1100RT at 20K miles was terrible on surging til I did the above.
Read the TPS voltage closed throttle on the red/white wire at the TPS connector.
Hmmmmm........ The BBSs were not too bad.Left side BBS was at 1 turn
Right side BBS was at 1.5 turns
Both sides now set at 1.5 turns
1) Make sure your valves aren't set too tight; .007 and .013-014 work better than the factory's recommendation.
2) Check the Zero setting of the TPS, and then the Idle setting, per Rob Lentini's instructions on the BMW Internet Riders site.
http://www.ibmwr.org/r-tech/oilheads/
3) Then do a super-careful throttle-body sync.
I've owned two of these machines, and I promise, I'm no kind of tech. BUT, that said, with the two 1100RT machines I've owned, this made all the difference.
I hope it's ultimately as simple for you.
Hmmmmm........ The BBSs were not too bad.
Make sure your intake valve clearances are correct with maybe a very slightly greater clearance (.001 to .002) setting on the right cylinder. Check the exhaust valves at the same time of course.
You should be able to use the BBSs for an equal final idle manifold vacuum setting. They don't have to be exactly the same.
Are your throttle bodies clean? Do you get smooth idle and equal throttle opening w carb stix? And do you get about 385 millivolts at the TPS wiper at closed throttle?
Otherwise, I'm outside my experience & speculative philosophy if you get surging with near equal BBS settings.
...... you should be able to get surge free operation after a anal intake valve settings, .......