Ahh.. hopefully this will be the last problem I come across in this install. My car has 2 cables for the antenna (maybe 1 for AM, 1 for FM?) and the AVIC-D3 only has 1 port for it.

Here's a pic

The one on the left fits, but the other one is too skinny. Do I just connect the one that fits and leave the other one disconnected? Car uses a glass antenna.

The big one that fits is the main antenna cable. Connect using that one. The smaller one is a backup antenna for my car. Nope, one is not for am and the other for FM. Just connect the main one and secure the other wire somewhere.

It's called a diversity antenna system. The stock radio uses the 2 of them to maintain the best possible am/fm reception. Plug the one that fits in and just tape up and tuck away the one that doesn't.

ahh so thats what it is called. Not too big on technical terms as you can see

Yeah not too common in domestics. Mostly seen in Mitsu's, Toyota's, and Nissans.

I had a related problem with my 2008 Audi A4. The installer gave up on AM and got me FM by using a Metra 40EU55 adapter.