The computer was purchased from Flagship One, a PCM rebuilder. It has been programmed to the vehicle VIN. And the VIN does match the vehicle because I thought the same thing previously.
I have erased all previous keys from the system after entering the security system (10 minute wait). Then attempted to program the 2 keys I have following the instructions on the Autel. I haven't run into anything that seemed complex which is why this is frustrating.
I have talked to a tech guy at Flagship One and he said the Explorer in that year span (06-08 I believe) are often incompatible with some of the aftermarket scanners. So I plan to use the J tool pass-thru and see if directly using the Ford website will work.
But, I am going to try to plug the old computer in and try it that way first just to be sure. The truck cranked and ran previous to the computer replacement.
I will post updates later, thanks for the info.
Or I'll post pictures of an Explorer engulfed in flames.