After corresponding with Garmin regarding my G3X/GTN 23/GTN 625/Vizion 385 interface, I went back today and changed some of the settings in each system. I still have the transponder message, but think that may be due to the way my particular system is set up. More e-mails heading to Garmin shortly.
I did get the autopilot set up and I'm amazed by the functionality of the system. I haven't figured out all of the vertical modes yet, but it will fly a heading, hold an altitude, and intercept/track a course just like the certified aircraft I fly at work...very impressive.