1) The antenna cable from the radio to the antenna tuner should be routed as far away from other wires as possible. It must not be bundled with other wires. I routed mine at the hull to deck joint as far away from everything else as I could and it helped considerably but not completely.

2) The ground from the antenna tuner is the crucial one. Be sure it is good flat copper, tied to a keel bolt (best for a Nordic 40).

3) The lead from the antenna tuner to the backstay should be as straight and short as possible - it is actually part of the antenna.

4) The power for the radio should come directly from the battery (fuse or C/B near battery) and should not go through your main electrical panel. Routed away from other electrical cabling is also a good idea.

5) Where is the compass sensor for your autopilot? Where is the autopilot brain? They should be far away from your backstay and antenna tuner as practical. Ideally the compass should be near the center of motion anyway.

The term ground loop in not necessarily correct. You have RFI getting into your autopilot. It may be the design of the autopilot. It can come from the DC wiring or through the air. Sources are not always easy to find. You may be able to stop the interference on some frequencies but maybe not all.