I just have this nagging feeling in my head that there are people here that are a lot smarter than me who looked at it this way and said, "That can't work, because..."
You are correct. "That can't work, because..." the computer will not function properly. You cannot simply re-wire the Ford's fuel injector wiring harness to match the Mopar's firing order without causing problems for the computer. I wish it was this simple, but it is not.
First, I'll try to explain the problem that is created by re-wiring the injectors. Secondy, I'd like to elaborate on the solutions to this problem.
When the Ford's computer adjusts the pulsing of injectors, it does not adjust each injector's pulse individually. Instead, it adjusts the four injectors on the left bank and the four injectors on the right bank of the engine. There are two O2 sensors; one in each of the dual exhaust pipes. These O2 sensors help the computer determine how rich or lean that side of the engine is running. The computer makes adjustments to the injector firing by adjusting each bank. Although the injectors are firing sequentially, they are adjusted to run richer or leaner in sets of four (on either the left or right side of the engine). If you criss-crossed the injector wires form one side of the engine to the other, the computer would be confused when it tries to make adjustments. Re-wiring the injector harness to match the Mopar's firing order would cause the criss-crossing of the wires from one side of the engine to the next. And, this would not allow the computer to function properly.
I worked with a GREAT Ford engineer on resolving the firing order issues. He originally recommended that I do not mess with the Ford's injector firing order. He said that it was fine to let the injectors fire in Ford's firing sequence, just make sure that the ignition firing order followed the Mopar's sequence. He said that this would function similar to batchfire injection and assured me that there would be no difference in idle or performance with the injectors firing out of sequence. Only an emissions sniffer would be able to tell.
Here are the three possible solutions to this issue:
Option #1: Follow the Ford engineers advice and leave the Ford's injector wiring harness and the injector's firing order alone.
Option #2: Rewire the firing order without criss-crossing the left bank and the right bank of the engine. This will result in having 6 out of your 8 cylinders firing sequentially.
Option #3: Have a chip burned for the Ford computer that tells the computer what is the new firing order.