Does the top cover on the inside of the car remain the same?
Yes you can use the same top cover, the bulges on the Mach equipped cars were purely cosmetic.
When you install/remove the box you need to remove the deck cover. Do not try to remove the deck cover without first removing at least one side panel.
Disconnect your rear window defroster so you don't knock the tab off, then remove the side trim (the plastic around your rear window), then remove the deck cover panel. If you try to shortcut it you have about a 90% or better chance of cracking your deck cover and the fiber "explodes" where it cracks so you can't just smash it back together and paint it.
Wiring is easy, and you can just leave the tweeters in place as a means of corking the holes they were in, or make covers out of plastic if you prefer. You probably won't be reusing any of the speakers unless you feel like making your own passive crossovers... which isn't a bad idea, just I doubt you'd be asking this question if that was something you plan to do.