Electrical 2005 GT WILL NOT START!!!!!

I have a 2005 GT with an SCT Livewire flash tune, BBK CAI and Throttle body. I don't use it much but my daily driver was in the shop yet again so I was forced to use her to get back and forth to work. Anyway, I noticed the check engine light was on and when I came home I hooked up the SCT to clear the code. As it was going through the normal process of uploading data I walked away for a few moments and came back and remember hearing a distinctive "click, click, click, click," in rapid succession from as far away as 10' from the car. Sounded as though it was coming from the engine bay. When I attempted to start it the constant "click, click, click, click" will not allow the car to start. This "click, click, click continues with the key in the on position or in the turn to ignition position, not quite as loud when turning to ignition though. The car has full power, radio, dome light, head lights, etc. I checked out quite a few other forums and thought that maybe I narrowed it down to the P.A.T.S. I changed the starter relay fuse, banged on the starter with a mallet, removed and had the battery tested, 648 cca on a 590 cca rated battery. Any ideas guys and gals? I went to the local Ford dealer yesterday and the Service Manager thought that it might be a voltage issue because the P.A.T.S. would allow the engine to crank just not start. (Alarm display is always displayed even with the key, chipped and non-chipped, in the ignition or out which is why I thought that maybe it was locked in Anti-theft mode). Really scratching my head here. I have her scheduled to be towed in Monday morning to the dealer but will try any last minute ideas before I have to take out a personal loan after their diagnosis.
 
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If the Anti-theft light is illuminated, I am guessing the P.A.T.S. system is having a hiccup. From my past expierence, if that light is illuminated, the engine/starter will not engage and the car will act as if the battery is dead(although the lights and instrumets all work).
 
If the Anti-theft light is illuminated, I am guessing the P.A.T.S. system is having a hiccup. From my past expierence, if that light is illuminated, the engine/starter will not engage and the car will act as if the battery is dead(although the lights and instrumets all work).
That's what I was thinking but the dealer seems to think otherwise. Guess I'm going to find out. Thanks though.