did you re-check the last one? i have a feeling is not the PCM (spidy sense) - oh well, it could be. if it doesn't throw a code you could use an external regulator (i think) but you'll have to make the connection and i wouldn't cut the wires just yet as it could be something else.
I would at least test the connectivity from pin 20 on the PCM connector (it's a Dark Green wire and is the alternator control driver) to the alternator - use a multimeter, and if there's no connectivity then there's your problem - if the connection is good then start the engine and measure the voltage you get to this wire at the alternator - if there's no voltage then yeah, seems that the PCM alternator controller is shot, if you get voltage then stop the motor and then put the ignition on - i belive in this case it should show 0v (i'm not 100% on this but i think if you have full 12v with only the ignition it means it's fried) - if all this checks out i don't think is the PCM but the alternator again or the connection from the alternator to the battery.
EDIT: there are 2 things that can go bad in these alternators: the brushes or the diodes - I don't think the PCM can fry either one of them (maybe if you have full 12v at the generator driver wire), but a short could also damage the diodes i think (on the 12v power wire that comes out of the alternator going to the PDC) - so you might want to check that as well, although in that case there are 2 x 50 amp fuses in the PDC that would blow so you would see that - very surprising that the first one you had tested bad after being on the Jeep.