Just wanted to give everyone an update.
So we got a used ECU off of ebay for a little over a 100. I removed the old ECU and double checked all of the grounds for it. Also check continuity on the black/blue wire at the ECU connector to the sensors and dizzy. I replace the heavy ground strap that was missing that goes from the cylinder head bolt to the firewall. Removed the splice on the splice off of the black/blue wire. Put the new computer in and it fired right up and idled great! Let it warm up and took it for a short drive. It ran great but the check engine light came on.
Check the codes and it was the O2 sensor reading lean. I sprayed water around the intake. It does not appear to be leaking currently. Took if for another drive and no check engine light on the second drive.
I don't think it had been running properly since the motor was changed out. When the intake was bolted up the gasket was not changed out. You could see were the gasket was compressed from the original intake.
It idles right about 750-800 RPM's. I think its good for now. If the intake does start to leak again I thought about getting two gaskets (one for an 89 and another for an 94) and a piece of sheet metal. I would use the 94 exhaust/intake gasket as a template for the ports and put that between the two gaskets.
Eventually we might change the cylinder head out for a HO one. Maybe this time next year. But as long as it not throwing a code and running good I think we are going to leave it alone for the time being.
Thanks for all of the replies to help me get this figured out!
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