If you do find out how to bypass pats do not put it on the forum, its because of the pats system that cars aren't stolen as often.
Use a mk5 loom and ecu on the engine will be easiest. If you have the pats chip but it won't start chances are its not wired up correctly but geting wiring info for pats it dead hard as can be only done by ford dealers with a chassis no for vehicle and job number before they can veiw the wiring.