HELP!!!!

I recently completed a body swap on my 4runner. For the body swap, I used the original wiring harness and electrical components. Now the 4runner wonÆt stay running. It starts, but dies almost immediately, maybe a second or 2. The check engine light stays on too. Initially, I pulled a code 6, but am no longer getting any error codes. A major problem could be that, during the re-installation, my friend thought the wire from the alternator was a ground and grounded it to the body. Not realizing the problem, I tried to start the truck and it wouldnÆt fire. When it fired for a brief second, the check engine light stayed on. Thinking it was just an air pocket in the fuel lines, I continued to try and start the truck with the same results. I then decided to try and pull the check engine codes (Code 6 was the output) and discovered the wrong connection to the alternator.

Now I fixed the alternator wire and tried to start the engine again, I got the same results. Now the check engine light stays on, but there are no error codes.

Things IÆve checked per the FSM include:

1) The computer. I tried a spare computer too.
2) AFM-Normal Parameters
3) Cold start injector-Normal Parameters
4) Main Relay-OK
5) Open Circuit Relay-Ok
6) Solenoid Resistor- Resistance was a little higher than spec.
7) I have fuel in the fuel return lines at the tank. So I donÆt believe I have a fuel delivery issue.

Code 6 is no signal from Ne on the computer, how do I check to see if there is a signal from the Ne. Any other suggestions??

Forgot to mention, it's a 22re.

Thanks,
Wilson