ground loop issue

A few comments on the schematic:-

  1. You will never read anything from the rotatory encoder because the arduino inputs go directly to ground.
  2. There is no pull up on A15 so you will not be able to read that switch state once it is not connected to ground.
  3. S18 appears to connect the CV to the Gate out, or Gate Out1 - is this correct?
  4. Not sure why R55 is fitted, it doesn't seem to be doing much.
  5. You can get + / - 12V if you have an AC output wall wart and half wave rectify the signal for each rail. Although this seems to be a lot of fuss for just one op amp. Maybe you could bias the op amp's ground to 2.5V but I haven't looked at the data sheet to see if that amp can work off +/- 2.5V or a 5V single rail.