I just did some research, and it looks like the Ford PATS system is a transponder-based system. Not easy to bypass.
Look at remote-start systems, they do sell PATS bypass modules that are basically programmed with the transponder code (2 keys required) and then there is a wire loop that transmits the transponder code to the computer. Nice hack.
However, there HAS to be a 5.4/4.6 computer that doesn't include PATS that you can use... again, ask the dealer's parts dept.
Good luck! And let us know how it works out and what you did to bypass it.
Can't you also get a spare key and have it set to full time disable it?..I went to a car audio place and they said to get an alarm/remote start they had to put a spare key in somewhere to disable the system...(may be cheaper route than to get another computer....