i believe the antenna is powered for am radio, not sure where it gets power from since the blue wire off the back of the radio harness is not used. but i definitely remember reading about poor am reception when that wire was disconnected.
as far as the rear speakers, i used low profile door speakers back there and they fit well, mine also had the two way tweeter that stuck out maybe 1 inch past the mounting surface of the speaker, so if needed you could probably put a spacer ring under the speaker to install it and get the magnet up off the fender