I assembled and disassembled several times and successfully shifted through the gears with the cases split. Without centrifugal force of the engine running and the output shaft connected to the chain / wheel you have to help the trans move from one gear to the other.
Did you say back apart?I just put all new gears on the driven shaft. ready to put into bike however it doesn't seem to be dry shifting into 5th. Is this something that requires tearing the motor back apart and re aligning the gears ?