I have been trying to think of what else could affect it.

I have put this car together with independent systems to prevent cascading failures.

The only thing the engine harness gets from the old car harness is the key on power in start and run.
I tied the run and start wires together under the hood to a relay and that gives 12 volts to the MS system.

everything else is just the engine harness.

power is new wiring independent of the old car harness.

I hate throwing parts, but other than temp sensors, the only thing left is the distributor pickup or the computer itself.