89 FZR Clunking noise

Hello everyone, just wanted to see if anyone would have some insight into an issue that Im having with my 1989 FZR600.

I bought the bike real cheap with a few sheared parts. The story was that the guys friend was doing wheelie when all of a sudden the chain snapped on it. It came through and sheared the end of the clutch release pin and shifter linkage. I have the bike running perfectly again but when its idling you can hear an intermittent clunking noise coming from somewhere in the transmission. As far as I can tell the bike goes into 1st and second gear, I havent had it out on the road yet to tell if it will go into the rest of the gears. Also, the clutch is real hard to disengage.

I know Im being pretty general but this is my first bike and have very little idea as to what to look at. Im a mechanical engineer with a lot of experience with cars so dont be afraid to get technical with me, lol.

Thanks a ton for any ideas/responses