mustangmike6996,
I too have an 06 Mustang GT and am looking for Sirius radio. I would also like to be able to hook up my IPod and control it by the radio.
Here's what I found:
If you want to stick with the Shaker 500 HeadUnit, then I believe you can just use the FM transmitter that comes with the Sirius receiver. You can get a FM Direct Connect to the antenna wire if you are getting too much static with the transmitter. If you want IPod connectivity, then I believe the BrandMotion Ipod connector will work (depending on your radio) and you can control your IPod through the radio.
It looks like I will go with a different HU. The Sony CDX-GT610Ui already comes with an IPod adapter and cable, and it has an aux input for the Sirius SIR-SNY1. If you get it from Crutchfield, the radio receiver comes with a mounting kit and harness, plus instructions. Didn't see the same deal on Best Buy's website.
Where do you plan on putting the antenna? I saw on a forum (can't remember if it was here or on another) that someone was successful putting the receiver under the plastic cowling below outside below the windshield. It was an older model Mustang, though, so I'm not sure if it will work with the 05+.
I may try to keep it inside the back window...but I heard that it cuts out pretty easily if it is inside. I don't really want to put it above the rear windshield like Sirius/XM recommends...don't want to break the car's lines up.