Sorry for the confusion...I'm having a hard time describing the issue because it's so periodic, and sometimes the car will start up and run like nothing is wrong, then other times I can spend several minutes cranking the car over without it starting.
When the latter happens, the issue of clicking and the other symptoms I described are present.
After I dropped it off at Ford and described to them the problems I was having(clicking sound, car cranks won't start/fuel pumps prime fine), They determined that there was a bad ground from the PCM to the CCRM. I purchased a new PCM, installed the chip that has my tune on it, and the car has not shown a hint of the initial problem, although it does not fire up now.
The only thing that has changed since the last time I drove the car home from the shop is a new PCM. I was assuming that the car not starting would have to do with the PATS system since the fuel pumps not priming had never been present until a new PCM.
I am unaware of how the bad ground was found, but Ford diagnosed my car and discovered a bad ground from the PCM to the CCRM...They said it was why the clicking sound was present and the car was exhibiting the symptoms of a bad CCRM...