First of all thank you for the response and I apologize about the confusion, I could have given a couple more details.
So in the MU2 preferences menu I have GTN750 selected. So it sounds like I'm getting this wrong, but I thought that the GPS screen below the GTN750 display was the 530. I do not know what to call that display. So whatever that is, it is clearly nav 2. So that being said I can confirm the CDI needle on the FO side of the aircraft does behave as I would expect, and how you explained. It functions as I would expect with a VOR station, and when I hit the CDI button on that lower GPS unit, it displays deviation from the GPS flight plan on that unit. I just now for the sake of troubleshooting confirmed this by programing in a nearby waypoint, pulling up the Xplane map and clicking and dragging my plane back and forth, watching the needle deflect left and right.
I cannot replicate this on the captains side using the GTN750. in VLOC mode it behaves properly, but when I hit the CDI button and switch to GPS source, I cannot get needle deflection not matter what I do. I put in direct to the same waypoint I used to troubleshoot the FO side and moved the airplane around just as I did, and I get no needle deflection.
And with the autopilot issue, I still believe it is related to this other issue. The last flight I did were I troubleshot it just a little bit, I noticed it kept just turning me off course by like 90 degrees, after being directly on course per the flight plan. Happned at different phases of flight.
Thanks again for the help!