All you can really do is trick the PATS system into thinking that the key is correct and in the ignition.

Ford changes wire colors every two or so years it seems, so if you want the simplest way to fix your issues, try and find the proper 99 harness if you can.

seeing that i thnk you work at ford i think you should be able to answer my question...i have a 99 4x4 auto b3000 that i just swapped in a 98 4.0ohv ....i swapped the tranny bellhousing and got a wiring harness off of a 96 4.0 auto 4x4 cause the motor came from a manual truck and also got the ecm from the 96 thinking it would do away with the pats system .....but everything is in the truck and it will start fine but when it is put into gear it sputters when you get on the throttle and wont shift and the theft light starts flashing ...is it possible to do away with the pats since i know the 96 ecm doesnt need it ....im having alot of trouble with this thing and any help would be great thanks kerry