Anti-theft engine swap

For what you are doing I don't think easy is a word to use. You have done the easy part already. Myself before starting this I would have found someone(s) who has done it before. Moving ahead I would put this thread on every known Mustang Forum and search the internet. Since they are two totally different harnesses and I don't believe they make an adapter harness for it you are stuck with crimping and soldering as far as I can tell. Good Luck anyway.

For the 1996+ model year PATS can NOT be disabled by "cutting wires". PATS is disabled by PCM programming.

BUT........please confirm if this is a "no crank" or a "crank with no start". Why is this important? Because let's assume this is a "no crank" problem. If so, then PATS is NOT your problem. Because Ford factory PATS does not disable the starter. It works by with holding fuel injector pulse.

Bottom line. Ford Factory 1996+ PATS does not take power away from any sub system when activated. It's only way to affect the motor is by with holding fuel injector pulse. Which this prevents the motor from starting due to a lack of fuel. I would assume that the Ford PCM is not handling the duties of engine management. Under this logic your problem is not "caused" by PATS.

IF this is a "no crank" problem then likely the problem is in the neutral safety (NSS) circuits. As the NSS do go through the automatic transmission or the clutch position switch (which do you have manual or automatic?).

Please clarify the base problem and explain how the engine management and factor PCM have been "hooked up" and let's see if we can point you in the right direction.

PATS can be disabled via a tune loaded to the PCM.

Again. 1999-2004 Ford factory PATS does not disable the starter. If you were to attempt to steal a stock 1999-2004 with a non chipped key, the motor would crank all day long until the battery ran down. As far as the starter is concerned the fact that the dash theft light is on is "white noise".

I still believe this is a neutral safety switch issue or there's a wiring fault in the NSS circuit. Does the starter relay in the battery junction box "click" when the ignition switch is turned to "crank"? If not, this all but proves that the starter relay isn't being commanded to close. The trick is to find out why.

Is there CONFIRMED power in and out of fuse F2.6 with the key in the "crank" position?

Has the clutch pedal position switch been connected and adjusted? Does it close (electrically) when the clutch pedal is depressed? The clutch pedal position switch is a just a simple open/close switch that closes when the clutch is depressed.

1999-2004 MY fuse panel schedule:
http://www.allfordmustangs.com/foru...r-swap-wont-fire-please-help.html#post2669271