Tentative solved! Want to test after a long soaking rain before I feel it's 100%. The small ground wire to the right of the intercooler (I believe for the hpfp) was particularly grungy. Sanded the surfaces clean, and put dielectric grease over the connection as a precaution.
Another update. Decided to undo, clean all the grounds I could easily reach. One by the battery, one near the intercooler, and two that I was able to access from under the car, near the throttle body? So far so good, but the real test will come when it's wet out.
Unplugged battery then reseated the ECU connections, and relays in the fuse box. Many of the relays were stuck in pretty good. The EGI main was especially tough and appears to have a discoloration on one of the pins. I am currently ordering a replacement one. If I didn't know any better the...
Update. I have noticed a faint ticking noise close to the ECU when the engine is off and cold. I am currently trying to locate it, but appears to be buried in a mess of wires. In the meantime I have flashed ecu back to stock to see if that was causing any issues. No change.