Car still won't start!!!

Typical Focus problem to begin with, the key wouldn't turn.  First we replaced the ignition cylinder.  Key would turn but car wouldn't start.  We bought a "key position indicator" or something of that nature.  It was a little black box that goes on the opposite side of the steering wheel.  Still no luck.  The PATS theft light is blinking like crazy now.  Things we have read say something about a PATS fuse but we don't have a clue where it is.  We are also thinking that maybe it has to be reprogrammed because some of the wires on the steering column got unplugged then plugged back in.  Any ideas?  We are trying to avoid towing the car to a dealership because my husband and I are stationed overseas and towing in Germany is really expensive.

The flashing theft light means that it is in antitheft.  If you have the original key (PATS with a large head and chip in it) then the system does not recognize it.  When you removed the old lock cylinder, was the black ring (electric) around the key tumbler assembly damaged or maybe disconnected?  This is part of the transponder system used in the PATS system.  That would be my first thought.  You have been working in that area, and the plug in on the transponder ring is rather delicate.  I have been doing this for 35 years and have damaged some in the past, just trying to unplug them. If you wait 45 seconds after you insert the key, does the flashing light go off?  The system should reset itself.  If it comes back on when you try to start it, then it does not recognize or see the key.