Perhaps check the VPWR voltage at the injectors while cranking. Reference the ground with the same ground as the PCM. There's usually a ground wire that attaches to the engine block or fuel rail for the injectors' ground path. The PCM will start to drop function at about 9 volts.
In general, since this problem started after installing the engine, verify that the PCM ground at the negative battery terminal, the sheet metal ground to the inner fender (or core support) and the main starter ground from the neg battery terminal to the engine block close to the starter are all intact.