Extremely difficult to diagnose something like this remotely, but I would be looking at the electrical system.
It sounds to me like you're dropping the spark on at least one coil. Try hooking a volt meter up to the coils, taping it to the top triple, and seeing if the display drops out at 5500rpm as you ride. It's unusual for a TPS to cause problems, although not unknown. However, rolling on and off the throttle appears to allow the motor to pass through the bad zone, so I suspect it's not the TPS.
If nothing has changed since the last perfect ride, and the last ride wasn't that long ago, then it's not going to be jetting.
The biggest problem is what you describe as bucking, someone else may describe as a judder, and someone else may describe as a misfire. Only slow, simple, logical methodical steps will diagnose this.
Start by eliminating the fuel. Drain/clean the tank and carbs, and refill with fresh fuel... whatever fuel you always use! If that's an AVGAS mix, then use fresh AVGAS mix, if it's 95/97/98/100, us that! Eliminate all variables.
Clean/replace the air filter. Replace the plugs and caps, shortening the HT leads 5mm before fitting the new caps. Check the LT terminals on the ignition coils and at the pulser coils, and the condition of the wiring from the pulsers. There was a good post by Dave Ett on checking the coils a couple of months ago. If it's still misfiring, then go through the harness, checking and cleaning all the connections and earth/ground points. Try your PGM on another bike (always preferable to trying a new PGM on your own!). That's all the easy stuff!
After that it gets expensive, and I'd be doing leak and compression tests. Bad compression, broken/worn ring(s), and duff crank seals can all cause the misfire too.
Again, it sounds like you're dropping a spark, but it's almost impossible to diagnose remotely. All you can do is work your way through the systems (fuel/electrical/mechanical) methodically.
_________________
Andy.
NSR-WORLD.COM
Please keep all responses to Forum posts on the Forum so that others may benefit.
Please DO NOT PM me for technical advice. My time is precious, and you will probably receive a faster response on the Forum anyway.
Check us out on Facebook! Please "like" our page!