92 engine in a 96 truck

REALLY long story short, a mechanic screwed up my 300 in my 1996 ford, and replaced it with a salvaged 300 from a 92. How much money will it be to get the ford dealer to reprogram the computer and change wiring harnesses to match the different model engine?

The engine is already in the truck, and I believe it still matches up with the tranny, exhaust, cooling, etc. it just has different emissions stuff on it.