I did a similar install in my VW (oh and in your's as well ;-)
I would just leave the stock speaker wiring in place and splice in the new wires from the amp. No need to run 4 pair from the seat forward, just tap into the rear sets at the rear, and then run 2 pair to the head unit and tap into the existing front set.

That way both are live and if you don;t have your head unit you can listen to the factory one, (although I wouldn't recommend running both at the same time) if you were really paranoid you could get the auto switcher from Sony, but if you don't really care then just you be carefull, You could always install a kill switch for the factory unit under the dash so there would be no "accidental" mishaps.

As far as the angle is concerned, disk is cheap, just make both empeg's a clone of each other, and when the HD in the one in the jeep dies buy a new one and swap it out.

Not sure about the venting issue, I think that holes in the Tuffy would defeat its water resistance capabilities. Probably best to leave it home when you go the beach on a hot day.

Peace!