There's one more piece that has to come out of the way. I'm pretty sure the gray plastic trim on the bottom has to be moved. It has spring clips and one or two screws holding it in place, and it only has to come off of the spring clips to give enough clearance for the box to come out. The wires and vacuum lines have plenty of slack to disconnect them, which may make it easier to work with. If I'm wrong and it's not the lower gray plastic that's in the way, then it's the speedo gauge cluster trim that's in the way, and that's held in with a bunch of screws.
My cylinder head overhaul: http://www.jeepforum.com/forum/f13/cylinder-head-r-r-picture-heavy-1348138/
My transmission overhaul: http://www.jeepforum.com/forum/f13/how-change-transmission-electronics-1560948/