Okay, so I was able to find two hours to mess with the Jeep. Plus it's getting cold. I find low temperatures have the ability to affect my list of priorities.
So here's the skinny at this point:
1. Fired her up and she's idling good, but there was a miss fire. I pulled the plugs and found them black and sooty. They were new, so I used a stainless wire brush and cleaned then re-installed them. Misfire went away. Put more coolant and transmission fluid in her, then slowly drove her around the apartment complex. Never went over 15mph or over 3k rpm. She never shifted. Boost gauge never moved. Turbo spinning and whirring sounded AWESOME. Misfire redeveloped. Parked her.
2. Fans do not seem to be coming on. I will double check the wiring and if that's ok, just wire the trigger wire for the relay into the "run" circuit.
3. Still need to address the "no charge" condition from the alt. Gonna start by making sure the battery is charged, then drive her to the local O'Reilly's and have them make sure it is me and not the alternator itself.
I've double checked the ignition at each cylinder by unplugging the coil over each cylinder, and I suspect but am not 100% sure about cylinder #2.
I used an extension to verify that each injector was firing in the proper uniform manner, and they all sounded fine. I also added sea foam to both fuel and engine oil.
I'm hoping that it's just the computer running too rich and fouling the plugs. Hopefully just driving her down the toll road for 20 minutes will start to affect things positively. Between the open down pipe exhaust, huge intercooler, weird exhaust manifold and evo8 turbo, I can imagine the computer is halfway confused by the signals it's receiving.