Keys stolen...now wont start..

My bet is that something happened when you attempted to "bypass" PATS. Perhaps when jumping the fuel pump you blew a fuse or burned something up. It seems reasonable to me that since the locksmith reports being able to program the new keys this tells me that the PCM and cluster is getting power. So the reason for the no start would NOT be related to PATS.

But why guess? Test. Turn the key on but do not crank. Does the theft light goes out after a 3 second "prove out"? If so, this proves the reason for the no start is not PATS related.

Given the amount of work done, IMO you should start by CONFIRMING power and grounds. Stop replacing parts. Test more. A common "plain Jane" test light will do more good than any "part swapping".

Confirm power in and out of fuse F2.34, F2,2, and F2.8 with the key on. Use a KNOWN good ground. What to do next depends upon the results of this test.

Double check the fuel rail pressure sensor (FRPS) is connected. Check for vacuum leak. Check for any disconnected sensors.

Review all of the information in the "crank with no start" check list.

1996+ Crank with no start check list
https://www.allfordmustangs.com/forums/4-6l-tech/336452-1997-mustang-wont-ignite.html

1999-2004 BJB CJB fuse panel layout:
https://www.allfordmustangs.com/for...r-swap-wont-fire-please-help.html#post2669271

Here's some information on a possible DIY PATS solution.

ForScan ODB2 scanner w ELM327 USB
https://www.stangnet.com/mustang-forums/resources/forscan-odb2-scanner-w-elm327-usb.57/