Magnum swap starts, does not run

Well, that didn't last long. It's back to doing the same thing.
I had swapped some wires around on the crank sensor to see if that was the issue. When I did this, the fuel pump would not even run. With the sensor disconnected then the pump ran with key on. So we tried a few more combinations of the wiring until we hit the one that let it run last night. It still sounded like it was missing on a few cylinders, but it was running.

I checked the wiring this morning to post up what worked and to my surprise, it was the same setup that I started with way back when I started this thread. Uh, what?

A friend of mine did this swap in a Jeep and said he had trouble with air in the fuel rail, so this afternoon I jumped the fuel pump relay and ran some gas out of the schrader valve to see if there was air. A few bubbles came out. Then I tried firing the car and it's back to running for a bit then chugging and dying.

I'm wondering now if the injectors may be clogged. This motor sat for about 2 years with the fuel line disconnected. A few months back I pulled the fuel regulator and it had some sandy dust stuff inside. I cleaned it out, but some of that could be clogging the injectors. Probably won't hurt to pull them and clean them out.

We were able to pull some codes out of the PCM this afternoon.
34= cruise control
53= PCM fault, I believe this is due to the computer not being able to communicate with the trans computer
72= Cat circuit
55= end of codes

Any other ideas?