Great - PATS problem

I have a 96 cobra and am having a bit of a problem and I believe it is with PATS.

I lost the main keys so I called a locksmith to cut me some new ones. Got that done and tried to do the manual program of the keys (insert key, wait 45 min for theft light to stop flashing etc.)

That doesnt work tho because the theft light only flashes rapidly for roughly a minute and does not display any codes after that either.

I had another locksmith come that said they could use a computer to program new keys. He said he was able to see the previous keys that were programmed and he was able to clear them to program the new ones BUT he wasnt able to do this because it would not recognize the new keys for programming. He suggested it was a bad pats antenna.

So i replaced the pats antenna with a new one and the theft light is still flashing rapidly with no codes. Used a meter to check for breaks in the wiring and all checked out good.

I'm thinking my last options are the stealership or a tuner to bypass pats. Any one have any suggestions, I am at a loss for words now.

Never reprogrammed pats, didnt know a way to do that or if that would even help

It's at Ford now and I asked for a quote to just replace everything, that should fix it right?

But he refused and insisted I instead pay the hourly rate to trace for a problem in the wiring because replacing the whole system may not fix it

Thats the thing not ford nor any locksmiths are able to program the keys

Ford wants to charge me $89 an hour to look for a problem in the wiring

The Locksmith told me about a lady the brought her mercury to the dealer for the same type of situation and it was 2 and a half months before they figured out what to do, needless to say I'm not too confident in just paying the hourly labor til they figure it out, that will end up more than the car is worth lol

So I was wanting them to possibly just replace the entire pcm/pats because I've read that is roughly $1000 for thrm to do and would certainly fix the problem correct?

Rather than them search for the problem while I'm paying $89/hr just for them to tell me it needs replaced anyways

Idk just my train of thought right now but I could be way off in my thinking, it's stressing me out

ended up being the pats module - $540