For my 2004, checked the battery terminals, disconnected to re-set the computer. Terminals were fine.
Something I've known for awhile, when the Yamaha shop replaced the TPS under warranty it was still acting up. At the time, the shop would not do any further diagnosis being the bike didn't have a throttle sync done. I ok'ed them to do it (cost over $100 and I wasn't allowed back in the shop to watch).
The bike still ran crappy, it later turned out to be the main connector under the tank that corroded and turned green (I found that thanks to this forum!) Cleaned and added di-lectric grease, been fine since(4-5 years).
Since then, I bought a
Morgan Carbtune for my FZ6 (vibrated a bit) and synced that. I later subsequently synced the FJR as well without problems.. I did notice, the CENTER BUTTERFLY ADJUSTMENT SCREW WITH A TOUCH OF WHITE PAINT on it (from the factory) was turned almost 1/4 turn CC (you can see the white paint on the spring, head of the adjuster and the base).
No one else worked on the bike...
Apparently that shop sync'ed my FI with that screw, NOT THE AIR SCREWS... 
Today, I checked the sync, it was off a little. I did put the center, painted adjuster screw
back where it apparently was originally set from the factory and synced from there. Got them all at idle within 2mm at just about the 25CM mark. Had some problems getting the idle to adjust, ended up turning #3 in, then out 3/4 turn per the manual and fine tuned from there. The bike still had some surge in neutral at 4k, little to none at 3-3500 RPM's.. BTW, the vacuum port caps were fine. I drained most of the fuel, put the bike back together and rode to the gas station for fresh Hi test. Seafoam/Chevron techtron and some other marine additive I use were also added..
The surge really was never noticed while under way (never has)but the bike was a little smoother after todays sync and did
power wheelie when it hit about 7k RPM (no clutch manipulation).
Anyway, guess its the nature of the beast due to the lean programming for the ECU...
BTW, my 07 Yamaha FZ6 will hold dead steady running in neutral at 4K- no engine mods short of iridium plugs.
I guess the FZ6 is set a bit richer from the factory as MPG's between both bikes are very close (each about 40 but I do wind the FZ up a bit higher, 14k red line).
Hope this helps
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Update 12-22-11, 1:00PM. Just came back from a test ride (from dead start cold).
With all the above done I've noticed the following:
(1)Cold start up, the bike idles a bit higher (since I've owned it new) and definitly smoother.
(2)The variation on the RPMs is back to normal, surging (in neutral) is back to normal, (maybe 100, 150 RPM
fluctuation). Normal riding is smooth as before...
Idles dead steady at 1100, no hesitation what so ever in throttle blips/acceleration (back to normal!).
