My 2002 (Yes we have had the FJR since 2001 here in Australia)I was having what I felt was a surge issue.
Holding the revs at about 2000 in first on a flat road (in traffic) the bike would begin to lurch.
I thought it may have been that the bike was running too lean and therefore I should look at the CO2 levels as mine is adjustable via the right hand dash interface..
Before fiddling the CO2 I had a call from the dealer mentioning that Yamaha has an international recall to replace the Throttle Possitioning Sensor.
I believe this recall is basicly all fuel injected yamaha bikes from 2000 to 2005. I believe there's a very good US site detailing the bikes effected by the recall.
Obviously this can't be your problem as it doesn't effect the 2006-> models.
CO2 could be the issue, as you say "running too lean". Before spending your hard earned green on accessories, I'd suggest taking it back to the dealer. After all it is under warranty.