If you did not replace any of the harness then you have to look at it as a 2002 4runner with a 2003 tacoma ecu. What that means is the only wiring diagrams you should be looking at is the 2002 4runner full wiring diagram and the 2003 ecu diagram, anything else is not going to help you. You are right about the clutch starting being simple, it should only be one wire grounded. I have a feeling you put a wire where it should not go so you need to go back to the basics. As for the 4wd I can't help you at all but I would disconnect that system and work on the ecu and clutch starting circuit first and get it running before trying to get the 4wd working