You can get real fancy with fabricating the mount but I've had great success with my NMO latch mount...Thin coax goes right in the hatch and then down the interior rear panel to my rig mounted in the PS rear quarter panel area.
Here is a thread where different antenna mounts on 80's have been discussed:
Not trying to talk you out of your idea at all, just offering some alternatives.
As for your other questions...I'm a HAM novice so I'm sure the experts will chime in but no, your antenna doesn't have to be "above" the roof line. Dead center of the roof will give you the best ground plane but that is an impractical location for many so you go from there.
I don't see any reason you can't make your bracket out of aluminum and yes, I would suggest a grounding strap vs. scarping the powder coat. Maybe a grounding strap from the base of the antenna then down the bracket and to a good ground location on the frame.
As for an entry point for the coax. I use the gromments in the rear area that can be accessed under the rig and inside the rear quarter panels. As Tim mentioned, you already have drain tubes going out these grommets so you can usually squeeze wires, coax, etc. through the existing hole in the grommet. In my case, I have my CB coax, Hoppy harness wires, and a couple ground wires all going through my PS grommet.