I"m pretty sure that you just unplug the skim module,install the used pcm,then program the new vin into the used pcm. The act of reprogramming the vin wipes the theft info out of the used pcm and when you cycle the key after programming the vin,if you leave the skim unplugged it should run and you should not need any pin codes.
The service manual recomends unplugging the ABS module while changing the PCM until you get it running on the new PCM.It has to do with the ABS module looking for the VIN from the PCM when you turn the key on. This way the ABS module will not recieve the wrong VIN from the PCM.