I just helped a friend with a whole engine / 6mt swap. We found that certains ECU file will not accept manual trans coding. His is an "L" box ECU- it would not accept manual coding so we wrote the manual file to the ECU using NEFmoto and no problem.
He wrecked his clockspring so waiting for another to finish the ABS/ S.A.S. calibration, but otherwise it was easy.

The car should definitely run and drive as long as the ECU has any appropriate file on it- doesn't drive as well because a couple inputs are missing (clutch pedal, etc..). But it'll drive.