Got everything swapped over this week. Mechanically, the swap was as much if not easier than swapping a 4.0 drivetrain back in. BTW, the motor mount brackets, crossmembers, exhaust, etc are all identical. The only things that are slightly different / need some modification are the throttle cable, fuel line routing in the engine bay, and possibly the transmission shifter cable. Use the vacuum/PCV routing from the 4.7 and everything hooks up like it was meant for it.
The engine cranked and started for about .2 seconds the first time and that was it. Now there's no fuel pump, no spark, nothing. The PCI bus is dead and there is no communication between modules. The instrument cluster is dead, my basic scan tool only sees "Engine RPM" and "TPS %". I tried my old PCM & SKIM and hooked up my scan tool and behavior was the same.
I towed it over to the dealer on my trailer and they were nice enough to hook up the DRB-III in the parking lot for free. Said the DRB-III had no communication with the PCM/vehicle and couldn't do anything. Suggested there is a short or mismatch in the wiring somewhere causing the PCM to lose communication. We talked about people having failed/shorted CKP sensors causing the same thing. The tech I talked to said he would unplug sensors & modules by process of elimination until PCI bus communication comes back online then make repairs from there. He did not think the 2004 4.7L engine in a 1999 4.0 chassis was the problem and said with a little wiring modification it should work perfectly. He said even still, it should start and run and just throw codes for the mismatched stuff.
At least I got all the mechanical work necessary done for doing the actual swap in the time and budget allotted in the shop. Now the Jeep sits in my uncle's backyard until we can get this electrical issue straightened out. I have to go back home to NC in a few days but he said the thing can sit parked there until the apocalypse as far as he cares. If I can't get it fixed in the next couple days I'll have to try again when I visit next month....