Update: I installed a new battery and tried registering it with the foxwell but it wouldn't work so I returned it. Took it to the Indy shop down the street (German Autowerke in Oceanside, CA) and he was able to get the trifecta off within a few seconds after registering the new battery to the ECU. Still had no boost and was in limp mode, luckily he was able to reprogram the module and boost was returned.
However, under moderate to WOT acceleration, there was a heavy misfire that would start with the SES Light coming on and going on to a CEL for Misfire CYL 1 if pushed hard. I decided to open up the airbox and found a bunch of sand and a really dirty air filter (bought it from an auction in the desert) so I swapped it out and there was a huge improvement.
There was still a small shudder at moderate acceleration, WOT was fine, but not enough to throw a CEL or even an SES light. I swapped out the Ignition Coils with Delphi GN10571's and the issue seems to be fully resolved now. This forum was a great place to help diagnose and wanted to update anyone who may also be experiencing this issue.