Josh says you must put the auto shifter assembly in the car, too. The ECU will not start the engine unless the shift is in PARK.
The car will start and run but will object to the fact that the transmission module is not telling it what gear it is in.

Josh says you should send him your "bad' parts and he can fix them.
OR send him the parts from the donor car and he can re-mask the ECU to be a manual ECU.

SOrry, the modules have a lot of brains in them, they expect to talk to the exact modules they were programmed for.