I have an '06 that is about 3 weeks old and has about 800 miles on it. Since I drove it off the lot the bike will surge in first gear when trying to keep a steady 20 to 25 miles per hour. Its next to impossible to maintain that speed comfortably because of it. I just got it back from the dealer from its 600 mile service and there is absolutely no change even though they supposedly checked this. I had also told them at the time that the bike stalls when applying throttle just off of idle when it is in neutral. Of course this didn't change either. Does anyone want to venture a guess as to whats causing this. Never having had an FJR before, I can't imagine that this in normal.
I have almost identical symptoms with my '06 - definitely surging or hunting in the low rpm range - somewhere around 3k. I also have the cough and die symptom. Seems to happen in this scenario - Ride the bike for awhile so it is warmed up well. Stop the bike - let sit for a short time - start up again. Bike isn't cold, but it isn't hot, either. Coughs just when you start to open the throttle. Usually starts right up, but once in awhile it coughs again. Had it do this 3 time at one intersection during the first week I had the bike. I attibuted it to learning the clutch and throttle -
since then - it has done it again - with clutch fully disengaged.
Have not done a TBS, yet and I think the bike does need it as it is a bit rough in places. have not run diagnostics on TPS, but will do that tonight. Have a tad too much freeplay in throttle and will address that tonight.
one other symptom I had - riding a couple of weeks ago through a fairly warm day - (about 90) - Rode it to a place and then cruised around a parking lot looking for someone. So bike definitely got hot. Parked the bike on side stand and left it for perhaps 1/2 to 1 hour. When I retrieved the bike and started it - it ran for SHIT. Very rough - like it was either starved for gas or getting too much. Felt like it was runing on 2 or 3 cyl. Reving the throttle seemed to clear its throat and progressively got better. Cleared up after maybe 5 or 6 revs - but sounded pretty bad. I would say that it sounded rich rather than lean. Didn't see any smoke or anything.
Cleared up and ran great for the trip back to hotel and then 350 miles the next day.
I would have said it was bad gas, but I had bought gas from a reputable station with lots of traffic, so the gas was most likely fresh - there was no truck delivering, so I doubt it was a stirred up storage tank.
anyway - cleared up and hasn't been back though I have noticed that after a hard ride when starting up - the bike doesn't feel like it has quite the same smoothness as normal. Also clears up quickly.
I'll address the throttle freeplay and check the tps this evening. TBS will have to wait till I dig out my carb stix (which I think I threw away when I moved) or the next service (which will be soon - currently 3200 mles)