Ok so today I put the motor back on the bike… put the controller on, set to 50% motor amps (250 amp max), and took my life into my own hands.
Now during the rides the BMS was cutting out the battery due to high amps (it is set to ~50amps). After a few runs I changed the kelly to only pull 20% battery amps and that stopped that. Tomorrow I will up that value until I find the highest value that does not shutdown the BMS.
I will also wire up the throttle and some switches to replace the control box.