Firstly - Ryan, that setup is awesome.
Second,
I actually just did this in my LR3, and I ended up mounting a cobra radio (not sure of which one at the moment) in the center console cubby box. This allows me to store the mic in the box with the radio, and still use the little cover over everything when it's not in use. When I need the radio, I flip open the box and plug in the mic. The lid will still close with the mic wire passed through. For the antenna, I used a similar setup to Nathan's with a small bracket that I bent mounted behind the driver's side tail light. I did use a "non ground plane" antenna (like for boats) since the roof of the LR3 is almost entirely glass, and there is no real reflective surface for it back there. Used it this past weekend, and it seems to function pretty well. It's dark here right now, but I can snap some pictures and upload if you'd like to see any.
-Paul