My thoughts...
I would not use 28 spline axles on anything bigger then stock tires. Thinking of the mid 70's when nothing had any power Ford still upgraded all the trucks to 31 spline. too many horror stories of 28 spline for me to want to run them.
With the 5.0 in place of the 351 I am betting the 4.88 gears will be matched really well. If you are going to do the 5.0 swap, hold off on the gears until you drive it with the 4.88s first. I always thought that rig was slightly overgeared with the 351 torque, 4.88 gears and the 33's. Thought a smaller motor would be perfect for this gearing/tire size.
The front is a Lock-Right. It would be easy enough to remove and put regular spiders in for an open diff. If you decide to keep the 4.88 in the red beast and move the locker to the toy that might be a better option. The detroit in the rear can be a bit much for street duty, I don't hav a good answer for what to do here until you drive it with the 4.88 5.0 combo and decide what you like. remember that the 9" housing has those axle wedges welded on for the torque arm, That will add to swapping difficulity.
For the history of that truck, the 351 is at least the 3rd engine in that rig I can account for; original, 302 freshly rebuilt with dual Edelbrock carbs when I first saw it, The 351 that is in it now. The Explorer engine would be at least #4 I can count.
For the 351, It is a '70 that I got out of a friend's '67 mustang (vehicle #2 at least), that went into the '69 (#3) , and when it goes into the crawler that will be #4 that I know of. The '67 mustang that the 351 came out of is still running around on a nicely warmed up 302 (at least engine #3 I can account for).
...And people wonder how much parts can be swapped around?