i wanna say check the spark plugs. did you clean the gas tank out thoroughly?

 

Yep. Tank was flushed good and proper while changing out fuel pump and plugs are all good.

 

Have you done a fuel pressure test? What is the tps voltage? Have you done a sweep to watch the range?

 

the fuel lines might still have some gunk in them. thats the only other thing i can think of

 

The tps range is 16 to 95 and were changed out with the recall. I haven't done a voltage check but will get onto that today. How do I test fuel pressure?

 

A Guage hooked online with the fuel line.

 

Also make sure your fuel line isnt kinked there is a mod for it here somewhere just cant remember where

 

Good day.
Have same problem: R1 2006, after 5000 rpm engine working with small vibration, and cannot run as same R1 in "good condition" (test on another R1 04). After motor heating up to 85-90 degrees, vibration becomes some stronger. If i stay about 3-5 min with working engine, problem go out for 100-150 meters.
EXUP working good, compression 14,1...14,3 bar in all cylinders, Spark plugs - new CR9EK, same color. Fuel pump replaced to new, all fuel tubes and injectors cleaning. New battery. No problem with engine start, no smoke. TPS working good (mark 4x xx xx). Find two owners in my city (Moscow) with same problem at R1 05-06, have no idea what could it be. Stock exhaust, no power commander.
Thanks in advance for help.

 

My R1 did something similar. Rough idle and very rough (to the point where I wouldn't ride the bike for fear of doing damage) when giving gas to the engine.

In my case, springs had broken and fallen out of the throttle assembly and they were not all opening and closing properly.

It was a $300 fix at the right shop that diagnosed the problem, but I wasted $1000 at a stealership that solved some other, unrelated issue.

 

No problem with springs, all throttles open and closing together (test with fully opening secondary throttles). I think that something wrong in fuel system, because motor working better with cold intake air (+15 C and lower) and become rattle with warm (+18...20 C and higher) air. May be injector cannot spray fuel good, just as single stream?...