P.a.t.s Issue

Turn the key to run but do not crank. Does the theft light go out after a 3 second "prove out"? If so then the PATS key has been read and accepted.

My vote is that you still have a battery problem. IE the battery voltage is not remaining high enough for the PCM to work during cranking. What is the voltage at the battery during cranking?

IMO every possible electrical problem should BEGIN with a through review of the battery and charging system. Don't let something as low tech as a battery be key to any project.

Here's some more information to review.

Howto perform charging system voltage drop test
https://www.stangnet.com/mustang-fo...perform-charging-system-voltage-drop-test.56/


1996+ Crank with no start check list
http://www.allfordmustangs.com/forums/4-6l-tech/336452-1997-mustang-wont-ignite.html#2984838

The round connector with the large black wire carry the CCRM and PCM grounds. These grounds are CRITICAL to the operation of the car's electrical system. A poor CCRM/PCM ground could absolutely cause the posted symptoms.

The Mustang has a ground system that bonds the battery negative to the radiator core support together. This in turn then goes to the round connector. From there onto the PCM and CCRM.

If asked to guess, the missing wires are part of the radiator core support ground.

The Mustang has used the same grounding system from 1996 through 2004. Do you have a buddy's Mustang to look at? Or how about a salvage yard in your area?

Another option is to look at the Ford wiring diagrams. If interested in getting a copy for yourself I maybe able to help. PM if interested.