Bingo, it was lack of 12+ going to the trans. For some reason I had that circuit wired to some power lead coming off the dash harness.. don't ask, I have no clue. I put the truck together 4 years ago while on a time crunch (baby coming), so while it worked flawlessly, there was obviously some goofy wiring done. It's all fixed now... sorta. I need to make up a small fuse panel, and eliminate the 2001 UBEC... but that's after the road trip.
Rough idle... I felt like a vacuum leak, so I checked the induction system I built (4" PVC), and then looked to see if the knock sensor wiring got underone of the intake runners where it seals to the head. Nothing there, but I noticed some of the foam they stick to the bottom of the intakes was sticking under the #4 runner. I pulled up the intake to find that most of the port was covered with the foam. I yanked that out, and things got much better.. but not perfect. When I was loosening up the bolts around runner #7, I must have bunped the foul PCV out. I reattached that... idles MUUCCH better now. It still feels rougher than when the motor was in the 93 Sierra, but that might be due to the mounts, not the engine. There is no stumble anymore off idle.
Took it for a maiden voyage to get some t-fittings to tie the steam vent to the overflow hose, and get some more distilled water to 50/50 up the Dexcool. Speedo dropped out, but the Tech II was still reading VSS, so the bridge connection at the speedo buffer connector must have come loose (it was just some MIG wire in there to test the circuit. Also, the HVAC and wipers don't work... probably a fuse, we'll see. The truck needs front shocks, maybe tie-rods and a centerlink too. I hit a few bumps here on our glorious Michigan roads, and the front end started to shake and the tires started to shudder. I checked out the tie-rods, they are a little sloppy, the centerlink has some play, but nothing that would make it shake like it did... I had to slow down to under 15mph to get it to stop shuddering. I'll be looking for some Bilsteins or Rancho's shortly.
More later, I took some pics of the engine bay about an hour ago, but I have yet to transfer them off my Blackberry.