The glove box is most likely water resistant and adds a layer of protection for the unit by keeping it out of the elements.
I'm not sure what the head unit you have currently installed looks like. I'm in the process of replacing mine, and it turned out to not be screwed in at all and simply slid out when I pulled it. If there is a dettachable face plate, see if there are mounting screws underneath.
It sounds like you're considering relocating the stereo. Personally I wouldn't only because it will leave a gaping hole where the old stereo was and require you to cut a sizable hole in the new location in order to flush mount. Plus, you'll need to re-route antannae, power, ground, speaker wires, etc. to the location of the new unit. Depending on how far the new location is from the old, you may need to extend or replace the existing connections. (I hate splices everywhere because it becomes a troubleshooting nightmare when things don't work).
You'd most likely need to make sure there's enough room to accomodate the new unit. I would hate to find out AFTER I cut a hole that new head unit won't recess all the way into it's new home.
Many new stereos have an remote control unit available as an add-on. I would think it would be easier to drop the new stereo in the old location and run a remote control unit to the dash. (If you haven't purchased the new unit yet).
In regards to the antannae, would buying an antannae mount that will allow you to drop the antannae down help the boat cover problem?
Ratcheting Rail Mount:
http://www.shakespeare-marine.com/mount ... unt=4188-S
Lift & Lay:
http://www.shakespeare-marine.com/mount ... ount=495-B
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