My bet is you forgot to plug something back in when doing the vinyl interior mod. The same happened to me.
if you are using the Y cable, and your phone appears as "ipod" under devices, then we know the USB part is working by your description. That means it is the AUX part that is not functioning if you can't hear any sound.
The exact same thing happened to me xD. Went on a road trip with friends. He connected his iPhone and we could navigate it, but no sound was coming out whatsoever.
The solution was to open up the small piece that holds the AUX/USB/Charger using trim tools. My AUX cable was not plugged in 100% all the way. I pushed it in deeper, and when I turned on the car again it worked.
You can also test them by just plugging in a ipod USB charger cable. if it charges your iPhone , you know the USB works. Likewise, just use an AUX cable and plug it into the headphone jack of your iphone. If no music comes out, then you know its AUX for sure
Edit: I don't think you need to remove the entire console... yet. First just remove that center trim piece under the armrest(next to e-brake) that houses the connections, and make sure they are nice and tight.
This is the piece I am talking about
