more info bro....yr and md....check plug ..compression and spark to begin with...

 

It's a 99 R1 With 50K kilometers. The engine was rebuilt at 41K by the previous owner. I'll check plugs tomorrow, but the have been changed 2 weeks ago.

 

Dont matter whats been done it the past ...a good clylinder needs good compression ...good spark...and good fuel....check all....

 

spray wd40 or similar on exhaust headers while the engine is running. It will turn to steam straight away if it's firing on that cylinder. This will tell you which cylinder is down. First check for a loose plug cap, try again, then the plug, compression test and if thats ok it's the carb

 

dont know...OP ...not responding....give it time....it seems

 

WOW!! My 98 R1 is having the same problem,I was riding then when stopped at a light it started sounding like it is was 250cc motorcycle,Going to check everything someone mentioned above.Hope it is something small, Cause my 07 is at the dealer right now for a possible valve guide issues,doing a similarthing,dealer hasnt say yet but I'm convince that what it is.

 

I got myself a 2000 R1 with a 2003 motor in it. I'll use it for now while I get my bike inside to check that out.

 

I had a problem whereby the bike just suddenly started running on 3 cylinders in the middle of a ride.

Seems someone had applied force to the lead at some point when removing the spark plug cap.

I trimmed 1/8" off the lead which exposed new copper, screwed the plug cap back on on and we have been running on all four cylinders ever since.