Since you replaced the PCM you have a vin mis-match between the PCM & PATS module, not a problem you just have to do the following steps, BTW: in PATS language WORKING keys means keys that will start the vehicle, not turn the ignition switch. If you replaced the PCM you won't have working keys. Also, and I guess you already know this, on this vehicle the PATS module is in the instrument cluster.
1. go into the PATS security module (connect a battery charger if needed to keep the voltage at least 12 volts)
2. select ICM/PCM parameter reset
3. select PCM/TCM parameter reset (if available)
4. exit security
5. look in the PCM. If you can find Keep alive memory reset do select it. (KAM reset)
6. exit diagnostics and wait 1 minute.
7. cycle the key to the run position(do not start) Do this 3 times for at least 30 seconds each.
8 after the 3rd time go back into the security module and erase all keys.
9. exit diagnostics and wait 30 seconds
10. cycle key 1 to run for at least 3 seconds then back to off
11. cycle key 2 to run for at least 3 seconds then back to off
12. again cycle key 1 back to run for 3 seconds then back to off.
13 vehicle should now start with both keys.
14 add additional keys using the procedure in the manual or let me know if you need to know how.
Thanks