A few updates.
Took the old Alternator to a local parts store to get tested. One store didn't have plugs for it, others didn't have operators that knew the tester, the 4th store was the charm. Alternator was dead. Ordered a new one and put it in, so that issue is closed.
Had a mechanic friend come by to help with some testing.
Revelations.
All the relays on the fuse box are good
ECU fuse is reading 12v, but ECU pin and software still reads 9v
All 4 injector pins on ECU also read 12v when key is on for power. Strangely their voltage is a true 12 unlike the ECU 12v pin. At this point not sure if the "12v" pin is input or output in the ECU
Both ECUs show same symptoms. After taking to quicksilver they are willing to test both ECUs next week so they are in the mail now. If they both pass as working means I have a likely somewhat simple wiring mixup somewhere.
With that said the new harness was questioned by my mechanic friend. The same pin that should be 12v input? On the harness is showing continuity on a fuel pump relay on the new harness so we aren't sure if it's setup correctly to match my current setup
So pending hearing back from Quicksilver