i bet it has to do with the pilot bearing it must not be right. did you have a hard time getting the tranny set back on to the motor? it sounds like the input shaft of the tranny is lodged in the crank/flywheel of the motor making them like one piece which would take the clutch out of the loop and make it almost to where it doesnt exist. do you have a good pedal feel at the clutch and can you watch the clutch fork have a good amount of throw down at the tranny. little more info please.