If you have the engine harness, IMO, the best thing to do is to get power to it, and run the engine with it.
Period.
Let the stock harness that was in the car, run the car, let the engine harness run the engine. don't overthink it.
That said, I tried something similar, and never could get it to work just right, and ended up buying the plug-n-play universal 5.0 harness from RJM. That one is perfect. You run a wire to key power, a wire to constant power, and a wire to your tach. That's it. You don't change a thing about your stock harness. That is how you are best doing it with a donor harness too, but I am wiring challenged. Best money we ever spent on that particular car was the RJM harness.
The donor car I was using was a Lincoln LSC. It had the 5.0 HO, but the wiring harness was HUGE and complex, and the engine harness was NOT kept seperate from all the 'other' wiring... so I had to try and extract the engine harness from miles of wires literally run in a spiral around the engine bay. I think I did pretty good, except for the fact I couldn't get the harness to work ever again. LoL It's probably easier using a Stang harness, but I have never tried anything the easy way.