I have a similar problem
I have a 2000.5 RSV1000, Ran really strong when I bought it, but smoked a little and smelled like coolant. On inspection I found antifreeze in the front cylinder. I dropped the engine, tore off the top end, Bought rings and gaskets from AF1 and put it back together. It has 190+ psi of compression front and rear. Timing is dialed in, throttle bodies have been cleaned and adjusted. runs and sounds great.... but when I take it out to ride it runs like CRAP! it feels, sounds, and acts like it is running on one cylinder, but both are firing.
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