I put mine in the saddlebag on my Tourer. Wiring is just like a car, & you can use the fairing speakers.

You can then use a Sony Marine remote, for control. It's below the speedo in the PIC. To the right of that is my XM/radio/MP3 player.

I suggest you splice all the wires so you can remove the saddlebag. My stereo splice is the white connector on the right. It is a PC power supply extension cord with 20 pins, and worked out well. (Thank you, Bigf) I cut the cord in half, producing a male & female connector which I then spliced into the stereo wiring.

Regarding your original problem, there'[s a connector in the fairing, and another under the right sidecover. I suggest you exercise those connectors, it may very well solve your problem.
Let us know how it works out.