mazda engine swap then major troubles
 

I have a 2001 Mazda B3000 and changed the motor due to it being blown. After changing the motor and using the same wiring harness! Now my theft light comes on and flashing rapidly. I had a lock smith come out and try to program a new key, but he kept getting a SCP message missing and it wouldn't allow to communicate to computer. I did not change computer in the truck. still the same one. With the original key the theft light flashes and the vehicle wont even try to crank, but i can jump the starter and it tries to turn over.

I installed a 98 ford ranger 3.0 motor into the truck, but used the original wiring harness because the transmission harness was not the same as the ranger.

I have exhausted all thoughts and need advise badly!

Sometimes they just lose memory programming if the battery is disconnected for extended periods of time. More than likely you will have to wrecker it to a dealer and have new keys cut and programmed.