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You will get transmission trouble codes and a constant check engine light likely. I don't know what that will do to driveability though. If it were for a non-electronic transmission, it would probably be fine, but since it controls the E4OD, I don't know what that would do with no transmission to control.
Did they ever put a MAF in the 5-speed 302 prior to '96? If I were to use the MAF system out of the Auto and use a 5-speed computer, would that work? What about using a Mustang computer in a Truck MAF system, of course changing the appropriate pins?
I want to say that there was a 302-5 speed MAF combination, but I don't know for sure. You should be able to use the wiring harness at any rate, and just change the computer. It should be easy enough to use the truck MAF wiring as long as you match up pins to the mustang computer. That should work fine, and while you are moving pins, you could just take out the ones for the transmission.
go here www.fordfuelinjection.com and read up . personally i think finding a mustang harness and ecu would be the way to go. or the guy running that site builds custom harnesses.
If you have access to a truck MAF harness, use it anyday before trying to splice in a mustang harness. The mustang ECU should match up after moving one or two pins, and removing the transmission control wires if it's an automatic harness.
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