I've have an 07 FJR1300 since Feb. and have put 20,000 miles on it. I've experienced many, many episodes of stumbling most of them associated with altitude changes.
Recent example:
During the Memorial Day 3-day holiday I rode from Seattle to Pikes Peak. I left work in the Seattle area about 3:00pm and rode (through the night) through WA, OR, ID, UT and entered CO on highway 70 from the west. At Grand Junction, I switched to highway 50 and made my way to Pikes Pike from the west, arriving at the park at about 3:45 CO time. After paying the fee at the gatehouse, I started up the Pikes Peak road.
The FJR didn't want to run under load. The speed limits on that road are as low as 10 to 15mph. I attempted to ride that slowly, but the engine kept dying if I let the rpms drop below about 4000. It would idle normally, and until I started engaging the clutch it seemed normal. But the second a load was applied, the engine bogged down and died. It took me more than 2 hours to go the 19 or so miles from the gatehouse to the summit. I did this by reving the engine to about 3500-4000rpm and slipping the clutch--constantly--to keep the road speed low enough to stay under the speed limits and make the corners. I had to stop, I guess, about 20 times to rest my clutch hand. The engine died about that same number of times. No indication from the instruments anything was abnormal--temp was always showing about 4 to 5 LCD segments. I think the park entrance is on the order of 7000ft; the summit is 14,110ft.
When I got to the summit, I had severe arm and leg cramps and a killer headache. I rested for a hour or so before heading down. When I started down, the engine seemed to work normally, that is, it would accept a load at low rpm and not die--but going down Pikes Peak doesn't impose much of a load on the engine.
During the remainder of the trip--up to Rapid City, SD then back to Seattle, WA, on highway 90--there were numerous episodes of engine surging: at constant throttle on essentially level highway, the engine would rev slightly, then stutter.
Other episodes:
This one I can usually reproduce at will, but not always.
I live near Monroe, WA; elevation under 100ft. I frequently ride up to Stevens pass, 50 miles away, elevation 4200ft. On that ride, say a 4100ft elevation gain, while riding up grade the engine often does the surge then stutter thing--at constant throttle going up constant grade, I can't keep the engine speed constant. Usually, when I turn around at the summit to head back down, the engine will not take a load below about 4000rpm for several minutes.
I've tried several brands of fuel. The bike's mechanic, whom I believe to be very good, can't find anything out of spec. Don't know what's wrong, but at times this bike is genuinely un-fun to ride.