Back a long time ago I had sort of similar symptoms - which I tracked down to worn insulation on a wire to #2 O2 sensor, which caused it to not work intermittently, so the engine went into a default map, at least on that cylinder.
Bike ran above idle just fine. Plenty of power, smooth, no excessive vibes.. so it wasn't valve adjustment or throttle-body sync.
I've been chasing this one for about a year - and finally today achieved success.
About 4 months ago I picked up a spare set of throttle-bodies with injectors, hoses, rubber boots, and idle/stepper regulators off Ebay. (It was one of those "got it so cheap I couldn't pass it up..) These have been sitting in the box they came in since then.
Today - as part of my 64,000 mile service, I decided to clean the idle passages in my throttle-bodies. Easy job to do - remove the plastic covers over the TB's (two T25 screws), then remove the connector from the steppers, and two more T25 screws, and they are exposed.
On oilhead bikes this was part of my regular 12,000 mile tune-up job. The oilhead used screw-adjustable air bypass passages to set the idle, combined with throttle bodies where the butterfly didn't quite close. The passages were fairly small, and the screws had a sharp tapered needle sort of end. Usually cleaning these made for a much better idle, and they seemed to get crudded up fairly quickly.
The hexhead (and I assume camhead) design uses a blunt sort of plunger/plug attached to the end of a stepper-motor screw, that extends or retracts in response to the stepper motor. The blunt plug has a slight taper on it, and goes into a large hole in the throttle-body casting that bypasses the butterfly. On the hexheads - the butterfly is completely closed (against a step in the bore) at idle. All idle air is going through the bypass passage and regulated by the stepper valve assembly.
So - what did I find? Cylinder #2 (port side) had a tiny bit of crud in the recess in the throttle-body, but IMHO, not enough to really effect anything. I cleaned it out with some MAF cleaner (good quality electrical cleaner that leaves no residue) and a Q-tip. I then looked at the tapered plug on the stepper assembly. There was some very slight rub marks on the side of the plug, but nothing really noticeable by fingernail. I took one of the "spare" steppers from a used throttle-body and looked at it. Same design, same PN#, different manufacturer I think, and where one had some black plated metal, the used one had brass colored metal. It had no scrape marks on the plunger/plug, so I cleaned this up and installed it (don't forget the O ring.)
I then looked at Cylinder #1 (starboard side) - no crud at all (but I cleaned it anyway) which I attribute to the port side being the crankcase vent side, this side doesn't see crankcase fumes. I took a look at my other spare stepper - and it had some rub marks on the plug/plunger, so I passed on installing it. But before putting the original one back in, I made a discovery..
Behind the plug end is a sleeve of metal (the black or brass part I mentioned.) Turns out this is spring loaded against the plunger, and serves to protect the stepper motor threaded shaft. It can be slid back about 1/4" with just finger pressure. When I did - I could see the stepper motor shaft was grease covered, and some of the grease had hardened up.
LIGHT BULB time! When checking my engine with my GS-911 I'd noticed the steppers frequently went out of sync at idle speed. I thought this was normal, and the ECU was telling it to. Turns out - that's probably not entirely correct. While the ECU can control the steppers individually - they are supposed to stay in step even at idle (and they're out of the circuit and locked above idle.) The GS-911 has a function allowing you to zero the steppers out (which is also done every time you turn the key on if you wait for the instrument dance to finish.)
I removed both steppers and re-lubricated the shafts. I have tiny little plastic paint applicators from EastWood auto - made for touching up rock chips in paint. They are a toothpick thickness plastic with a tiny little fuzzy end (meant to pick up a tiny bit of paint and precisely fill the rock chip.) These seemed perfect for the job.
I used some synthetic moly grease from RedLine. I chose this because I know it holds up and stays fluid for a LONG time, and it seemed the right viscosity for this application (a WAG, but it worked.) I used the paint dabber to get the grease down along the stepper motors threaded shafts.
I then reinstalled the steppers, and first ran the ZERO step function on my GS-911 to distribute the grease, and then another function it has to "exercise" the steppers (it's a stepper actuation function, where they just cycle open/closed for as long as you enable the function.
Finally I started the bike. SMOOTH idle. And the steppers were staying in sync according the the GS-911.
Did a test ride to a mechanic friends house, who had previously commented on my crappy idle, and as I rode in he asked "what did you do to the bike?"... It's really that noticeable.
Harry - if you want to stop by some afternoon we can do yours.. take about 15 minutes now that I know what needs to be done (and you're at about the same mileage as I am..)
If anyone is interested I'll try to take a few photos of the spare steppers, showing where to lube them before I put them back up on the shelf. Lemme know.
Happy happy! And my new EBC rotor came for the rear, so I have another project for tomorrow.. Retirement doesn't get better then working on the bike and taking test rides.
PS - update - a friend who not too long ago bought a used '07 R12R with about no miles on it also experienced the rough idle and occasional stall. I gotta send him this link.. (Hi Fletch!) It appears time is probably the culprit in the grease hardening up, not use.
I would have never thought about this ....
