I still haven't figured it out unfortunately.
The car seems okay so far except for running lean at idle, running rich at throttle and stumbling at 3-4k but I'm chalking that up to a boost leak for now.
I thought about contacting Ash about it but it's been so long and he's such a pain to get a hold of.
Once school gets out and I have some free time I plan to socket my stock ECU and throw the chip in there to see what happens.
As for the grounds the FSM located
here has diagrams of engine and chassis grounds for each harness.