I've mounted antennas behind sunroof's before. There's usually enough clearance between the mount and the glass for the sunroof to retract with no problem. drill holes. Don't do mag mounts, etc. You wouldn't believe the performance difference between the two. Appearance is also another thing that's important!
My suggestion is to mount your antenna, run your feed line, and your power from the battery to the place where your going to want your radio. Don't tap into any other electrical sources. Run straight to the battery with a circuit breaker in line. Ground to the chassis with a fusible link to the negative end of the battery. This way, if you ever have any type of electrical drain, you'll be able to rule out the possibility of it being any of the thing's you've installed. It also makes it easier for Ford if it's ever got to go back to the dealer. Those are the biggest things. Figure those out and then once you've got that figured out, then your good. Any other questions, feel free to ask. But just so you know, if this is your first time doing something like this it's going to be a little hard to understand with us telling you over a computer. But there's alot of people here that are better at explaining stuff then I am anyway...
