2001 Honda TRX450S FOURTRAX FOURMAN S???
Maybe something fell into the engine while you were rebuilding

On my wifes ltr450 you have to hold the clutch in to start it...
People say that oil can make an engine act up, but it seems to be mechanical. Most of the time there is a reverse switch that could go out. My trike lost 2nd gear one time and I opened it up and everything looked good(gears looked perfect)....sometimes shift forks bend.
It could be #5: DRUM, GEARSHIFT= If there is anything wrong with it replace the whole Drum. Good luck
GEARSHIFT - DRUM - 2001 Honda TRX450S FOURTRAX FOURMAN S