I just want to make sure you have some sort of plan before you just start pulling pieces off the car. Honestly, I would get it running right first... you don't need to add anything to the equation.
Backing up a bit here, why did you need to redo main engine harness?
I am starting to think there are larger issues here - in particular, I would recommend that you confirm that all connectors have been routed to the right spot.
Backfire/popping sounds like a timing issue - was the timing chain off at any point while you had the main harness disconnected?
okay the only thing i have done to the car so far was replace the spark plugs and the starter, i also replace the gaskets for the lower and upper manifold, ran a straight wire form the starter to the alternator the same gauge that was on it originally, and i replace alot of old bolts, but i never took off the clinder head cover or anything inside there or the timing chain never messesd with any of that,
what do you mean by redo the main engine harness?
i didnt think i said i was going to
in order of what i did,
1/2. took off air intake
1. took off upper manifold
2. took off fuel injection
3. unplugged feeds to sensors and regulator like idle air control valve, knock sensor
4. moved octopus of wires
5. took off lower intake manifold
6. took off starter replaced it with new one,
7. ran new wire from alt to the starter,
8. replace gaskets on lower manifold
9. reinstalled #5-1 in reverse order
10. put a new gasket on upper intake.
11. changed spark plugs
note that i never took the throttle body off, left it attached to the uper manifold i fliped it upside down and moved it out of the way, also i check all connections and vac lines