Something just popped into my dusty head. Has the battery been disconnected for any length of time since the start of all this trouble?
What I'm getting at is that it's possible the ECU is stuck in some stupid state due to the spike in voltage. It has a capacitor back up that will keep the current memory state for about 15 minutes or so. It might be worth disconnecting the battery for an hour or so just to see if that makes a difference.
Contact the folks who have done engine swaps from a 3FE and try to borrow a known good ECU. Contact cruiserparts.net and see if they have a 3FE ECU out of an FJ80 for sale. The ECUs from an FJ62 are a different part number IIRC. I might still have my spare in the garage somewhere. If I do you're welcome to use it for troubleshooting.
What I'm getting at is that it's possible the ECU is stuck in some stupid state due to the spike in voltage. It has a capacitor back up that will keep the current memory state for about 15 minutes or so. It might be worth disconnecting the battery for an hour or so just to see if that makes a difference.
Contact the folks who have done engine swaps from a 3FE and try to borrow a known good ECU. Contact cruiserparts.net and see if they have a 3FE ECU out of an FJ80 for sale. The ECUs from an FJ62 are a different part number IIRC. I might still have my spare in the garage somewhere. If I do you're welcome to use it for troubleshooting.