Noise from transmission

Ok guys. I have a 2002 cr250 engine out of the bike and the clutch case is of. When i spin the mainshaft while the engine is on the workbench straight it sounds fine in neutral and in gear, but as soon as i lean the engine over to the right then spin the mainshaft there is a clunking noise from the transmission and it feels like the mainshaft is being slightly caught on something inside the transmission. The previous owner done a rebuild on the engine, could he have left a washer out of the transmission or is this normal. THANKS ALOT.

UPDATE...just checked it further and 1st and 2nd gear clunking then 3rd is clunking and stiff to turn and 4th and 5th runs perfect