I'm fairly certain mine are 5 and 3/4" inches for the front doors and rear shelf.
Do a youtube search for E39 speaker change - there's a couple of great videos showing how to take the door cards and back seat/shelf out.
Rear speaker change involves back seat (base and back) remove, as well as the C pillar trim/light assembly!
Front door cards are easy to get off - getting new/better speaker cable through is a different thing. There is NO space behind the trim where your right foot is.
I ran cable out from under the dash into the open door and behind the door trim very close to the door hinge. Taped it close to the rubber boot for all the door electrical cables and it doesn't get cut when I shut the door.