OK, so you have a new computer. ECU/PCM/whatever - we are talking about the same thing, I hope. (not trying to be annoying, just want to ensure we're all clear.) What was the programming on the new unit? Stock or Lund?

Here's where I'm going with this: if it is stock, and the DS bank shuts down, there has got to be a mechanical reason for that. I do not believe (and I may well be in the minority, or flat out wrong) that this is an electrical/electronic problem. I keep thinking fuel, but you don't seem to be getting lean codes. It started out OK, i.e. started and ran as you indicated, so that tells me the electrical stuff is OK. It would tend to tell me fuel, because it would take a few rpms for the fuel problem (i.e. a blockage) to come into play.

I try to stick to fundamentals. It is either fuel or spark. Or compression. If compression is bad on a brand new engine, you need to send it back. Or it's the the cam, most likely. You've done your homework on the electrical - it certainly seems like that part of it is covered. Maybe the tune, but you had similar issues, apparently, with the factory tune.

Please prove me wrong, but I gotta believe this is a fuel problem. Or the wrong cam, but you'd probably have a damaged piston by now.