I own a 2000 mustang gt 4.6 and i just swap a 5.0 stroker engine-tranny-ecu to it but when i try to start it the theft light comes on in my dash any ideas?
For such a swap as this you are going to need to include a TON more details.
If you are using a stand alone engine management system then how could the PATS system on an PCM that's not being used be preventing the motor from starting?
The first trouble shooting step for Ford Factory PATS system is to turn the key on but do NOT crank. The theft light should turn off after a 3 second "prove out". What does yours do?
Remove everything from the key but the key and try again.