I'll toss in my two cents as I am building an overland BII myself.I would first decide on the weight of vehicle and tire size. RTT? Bumpers? Fridge? Overlanding gets heavy and will effect your suspension choices. Tire size will also factor into suspension and axle choice. I am sticking with 31s and possibly going up to 32s, but no further. I live in some very harsh terrain and I can wheel 80% of terrain around here on 31s with a winch and patience. i have a Tacoma for serious wheeling and that is a whole 'nuther deal. Personally, I don't think you need huge tires for overlanding. I live in the Granite State, so my opinion here is valid lol.
OK, so axle choice. I have the D28/7.5 combo right now and I am gonna stick with these until they break. After they break, I will replace the D28 with a D35 and I will keep a 7.5 if I can find one. If not, I will upgrade to the 8.8. I would stick with the D28 forever as it plenty strong enough for 31/32 inch tires with careful use (i.e. using a winch when necessary, etc.). However, aftermarket support for that axle is awful. You can find bearings, rotors and seals, etc. But if you want a re-gear you are out of luck. There are also no lockers that I am aware of for that axle. So, when the D28 goes, I will upgrade to the D35 simply for the fact that I can more easily maintain and modify it if I want to. The 7.5 is plenty strong for overlanding and aftermarket support is still there, so I will stick with that unless I simply can't find one.
What should you do and when? All of it at the same time IMO - if you know what you are doing. If you don't know what you are doing and just learning, you will end up bouncing back and forth between jobs, and thats OK, gotta learn somehow. Don;t forget sway bar bushings, axle pivot bushings, seals, bearings, etc. I did mine piece meal and I have wasted a bunch of time going back in to fix things I should have fixed the first time I opened something up. For example, when you change the suspension up front, change all bearings and seals, rotors, brake pads, do the radius arm and pivot bushings and re-bushing your sway bar, etc, etc, etc. Don't play around if you are going to overland. You want reliability, and you are working with a 30+ year old truck. In short, replace it all! Trust me I am learning the hard way lol. However, if you are new to this stuff, I would do things one task at a time so you don't screw things up.
Sean