Unfortunately the manual was just short of useless...But
I managed to get ahold of a dealer in WVA, Louisville and Lexington are CLOSED on Monday.
The dealer was able to find a similar unit with a Red/Blue cable and identify the BLUE wire as the ground side. I matched Blue to Green and put the RED to the other pin and now It is wired back correctly. And I taped the pins with self bonding tape so it won't come loose again. Unfortunately that relay doesn't work, due to a missing/failed command line from the ECU. I verified the relay by simply removing it and shorting the contacts and then listening to the Fuel pump start to hum.
You are right about the ECU.. It is mounted under the dash on the drivers side. I cleaned all of the contacts with DeOxit but it didn't fix the Fuel pump.
I guess next is to remove the ECU, open it and see what kind of damage it has. That should be fun. At least I understand Electronics.