Teige; we're making progress, but this is about as far as I can be of much help. Hopefully, Mica or one of the more electronics-savvy members will notice this thread and step in (which is why I moved the thread here where it's more likely to draw that kind of attention).
If you have a multimeter, it seems to me that the next step would be to test the signal coming from the PF-6 card to the controls (the ribbon cable splits with the neck signal going one place and the bridge signal going another). If the signals are the same, then the PF-6 card is fine, if they are not the same, then the problem is in the PF-6 card. However, I don't know enough to tell you how to do that test. If the PF-6 card tests fine, then you would continue testing the circuit on each side until you find the point where they differ. But again, that's beyond my skill level. My guess is that Mica or one of the others will be better able to quickly zero in on the problem or suggest the next action to take.