First thing to do is to check the fluxgate compass
. It is the easiest thing to do and you can do that and not screw anything up. What you do is in mount it and if there is enough slack move it so you can sit in the slip and turn the compass
in set increments first clockwise and then reverse. The reading from the helm
should follow smoothly.
This may seem all too simple and obvious but it's what my good friend that has been working autopilots since they were invented did for me when we had a problem. It really is unimportant that it used to work. You need to start with the items that may actually be fixed. This will validate the auto pilot and then you can move on to the GPS
Personally, I never auto pilot to a way point as a cross current
can get you screwed up pretty bad. I would start by asserting that the autopilot can navigate a course without the GPS
to divide the problem into one half that works from the other half. I also would hesitate on ripping anything apart since it is easy to avoid the real solution and make the problem worse or at least more complicated. If you can validate both halves then the link between must be the problem.