If you still have the GPS-250, it has an issue with the calendar roll-over that happened last month. A fix will be out shortly, according to Dynon support.
http://dynonavionics.com/cgi-bin/yabb2/YaBB.pl?num=1556055232/17#17
Have you toyed with the style and size settings in the EMS page configuration?
Some of what you saw from MMarien was custom changes to the configuration files, as mentioned in his posts.
The default squelch level is 50. I had to bump mine up to 70 after installing LED landing lights in the wings, which do not use shielded wire and have no return ground. Everything still works well but the radio no longer breaks squelch when I turn on the landing lights.
Set it as low as you can...
The 440 feeds GPS through a ARINC box 429 for navigation and AP but has a separate serial feed (TX) to the 261 transponder. I suspect the latter is your issue.
Contact Dynon support directly for this. They'll want to see the logs so grab a copy first. The logs will help diagnose the issue. Also consider installing a backup AD-AHRS.
It is okay to run the wire to any good ground. I typically run the PTT ground to the mic jack ground, depending on which is easier.
This ground for all the other functions simply trigger a relay to do something, so it won't interfere with commo.
I wouldn't consider "all over the place" normal but I don't have experience with the D180 system. Is there nothing in the install manual on this? I suspect a protocol setting is incorrect on one side and/or the other.
I'm with @kelllym on this one too. Plus, with the ADSB-472, it sends traffic and WX to Foreflight, which has audible traffic alerts if you have a BT headset tied to your iPhone/iPad.
Last I read (here) it was not planned to be in the next software release but, at the time, that release was expected by EOY 2018. Hoping they get it in 15.3.5 too.
What version software do you have installed? There was an improvement in this area for version 15.3.3.
Improved: Tracking of lateral guidance by the autopilot when on the final approach segment of a precision GPS approach.
I'd start by confirming you have +5V on the position sensor white/orange wire and a good ground on the white/blue wire. Moving the sensor should result in a variable output on the white/green wire.
I believe russp is correct that the Level button on the AP button panel only works in Expert Mode. This change has been requested in the past. I think you can wire in a separate button to work in simple mode, though.