1. Did your factory radio have 3 connectors in it? Mine did (2008 Mountaineer w/Sync and Nav) - see picture. So I didn't have to think about this, if you didn't have 3 connectors in your factory radio then maybe you don't have to do anything with that? I'd maybe email their support or read the manual that is available for download online.
2. What colors are the wires? Can you be more specific, I had 1 wire that I didn't connect. It was to the Sync harness because I was done with Sync. Sync didn't work well with my Iphone 6s so I didn't retain the function.
3. For me to retain the original Aux headphone jack connection I think I would have had to retain Sync. I ended up routing a new USB cable to the center console and skipping the Aux because again... Wasn't planning to use that either.
I'm not of much help to you I guess because applications are different as are expectations. The Maestro Idatalink has a forum where you can ask specific questions for the installation or search it for your questions. Does your new deck have Nav? Does your truck have a Sirius radio antenna? If so, reference my post from a month ago about the adapter plug I found, it was really slick for installing and not using the aftermarket GPS antenna.