So I've been working with Sequential to sort of some of my Pro 3 SE issues. So far they've been really responsive, and we've managed to get at least the Pitchbend Wheel issue sorted. Basically the pot for the wheel was loose in it's mounting bracket, so I had to take things apart to tighten it up. I'm impressed with how well the Pro 3 is built (other than with the person who was supposed to tighten things!) now that I've opened it up.
I also decided to try looking at the cutoff knob to see if maybe just reseating it or something would solve that last issue with my SE. Sadly, still no luck so they are sending me a new pot to try later this week. Happily the pot for the cutoff is mounted by itself right to the front synth panel, and not part of the circuit boards.
Here's a few pics of the inside for those that are curious:
IO board:
The assembly for the PB and Mod wheels:
Solitary filter pot: