I like wheelbase when doing off-road -- so for me, the 4 door is the better shake. One advanatage of the 2 door is that you can trim the rear fenders more for tire clearance.
The BII, in my estimation, is too short to be decent off-road. I know a lot of BII guys will probably chime in and say otherwise, but they are Jeep CJ short. I don't like spending time upside down myself, so I like the stretch.
Five Speed (M5OD) is definitely the stronger platform, but the auto will work fine with a cooler. Unless you're doing mud bogs or desert work, the transmission really isn't the weak link anyway. It barely gets a workout in off-road driving, mostly in 1-2 going slow. It is when you're trying to run 80 mph up big/long hills in OD that you smoke the transmission. Ask me how I know (and yes, I wheeled a 1st gen 'Sploder that I also drove on the street -- only went through 3 transmissions -- all street failures, not trail). Making the swap to the stick can be sort of a pain -- lots more parts than most guys think -- but otherwise the way I'd go.
My current build will run a C4/5 w/manual reverse shift full-hold in all gears transmission. If I get in trouble with that, I'll switch to a stick, but I think I'll be fine. Autos are the easier-to-drive setup off-road, in any case, unless you really do some gear work or get a 4:1 transfer case. I've watched a LOT of guys smoke clutches, hop up and down on hills, etc., all while "thinking" that they knew how to drive their manual shift trucks. Turned out, they had a toe on the clutch pedal all the time. Get them to leave that foot on the floor and all is good.
4 liters make noise. Get used to it. The way I figure, while they're making noise, they're running. When they get quiet, they're done. I ran Amsoil in mine -- helped a lot with the valve noise, but never got rid of it. Lucas can help also. Run Lucas in the steering pump also. Helps with that stupid whine (or replace the pump with a saginaw).
You definitely don't want to run the 7.5 and Dana 28 axle setup, no matter what. If you do, carry spares -- in the truck -- and make sure you do the C-clip eliminator spring mod so you can swap the axles out on the trail. You'll have to. For any Dana 28 guys reading this, PM me. I have 3 sets of lockout hubs for sale.
I laid out a set of steps to getting a good suspension using mostly salvage yard parts in this thread:
http://www.explorerforum.com/forums//showthread.php?t=237302