Q: Car will start but will not stay on

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I have a wrecked 96 4.6 auto Ford Mustang, I just put the motor in a 98 4.6 manual body the car will start but will not stay on. Mechanic took to dealership for programming, They said they could not due to wiring. What could be the problem? My mechanic is telling me that the 96 motor and 96 computer will not work in the 98 body and wants me to get a 98 computer. He is using the 98 key. At this point, I am confused.
My car has an automatic transmission.

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