Have you checked the MAP sensor? Vacuum? What's your fuel pressure at the rails?
I'm not saying the PCM isn't bad, but it's pretty far down on my list of suspects for being down on power... But, since you have a bad component, definitely get it fixed... If it's a single bad cap, is it in a spot where you can just solder in a new one?
I don't believe pre-OBD2 PCM have any sort of VIN association, but there is probably different programming based on it's configuration, such as GVWR, A/C vs no A/C, EGR etc.
I'm not sure what you're saying about the shifting.
2000 E450 dually V10 wagon