Cole,
I’m sorry about your VPM-1 issues.
U2 is labeled on the voltage chart. It’s the IC in the middle of the board. Make sure the pins are -9v and +9v, as labeled.
You pedal’s symptoms are odd. It kind of sounds like the microcontroller may be screwy. You may want to do step D-3…it could fix the issue. The other thing to check would be to ensure the LEDs in the optocouplers are orientated correctly…the long pins should be in the square holes. Check that stuff and report back.
-Brach