Altinator & PCM problem.

Last week while driving home in the snow, every light on my dash came on, the car started jumping irratically, then it died. It's dead. So, I had it towed into PepBoys thinking it was the altinator, I was right, it was, but here's the brunt of the problem. PB's says that the PCM is not reciving 5volts, and that I need to have something re-flashed. So they replaced the altinator, and I brought it to the dealership. They said that the altinator is fried, now I have to bring it back to PB's, have them replace the altinator, then bring it back to the dealership to test for the PCM I smelled what I think was wire casing burningwhen the problem first started. Any had this problem before? What did you do, and how exactly did you get it all resolved. Thanks.