Help with stock EFI

OK, so it's still wired to the factory reverse light switch. I think that is mounted to the steering column itself, unless the car was a floor shift setup originally.
Find the reverse light switch in the car and see if the factory shifter is still operating it correctly. Should be a two wire switch. Lights should be off with switch unplugged, no matter what. Switch could be damaged or not functioning, or maybe the column is not moving the switch properly after the transmission swap.
If the switch is not working or the column is not moving it correctly, you could re-wire to the current transmission, which has the reverse function built into the three pin connector.