Boxing will accomplish all you want in the rear. I would only add additional plate where the rust issues are. Maybe one more over the cab/box interface.
2 people can remove a bed, 4 makes it much easier. I'd recommend 4. The bed does not weigh that much, but I prefer the control 4 people gives, to prevent damaging the bed by smacking things, etc... Also, a set of sturdy saw horses is key. You don't want to just set the bed on the ground.
A day is certainly doable, provided there aren't major issues. If you are set on a 1 day turn around, plan to start early, and before the day, make sure you can get all the bed bolts loose, find and disconnect the body harness (tail lights, etc...), and pull the filler neck. That way if there is anything stuck or siezed, you can get it hit with penetrating oil, and go get spares if something breaks.
If anything is too siezed, or it get to be too much, the bed can certainly be left on.
Also, pull the shocks out, don't want hotness around those.
Anyway, that's how I go about getting a quick project ready, by trying to think through problem areas (rusted stuff) before hand, and get after it so I go into the project day prepared.
Anyway, thats all just my .02. Certainly take it for what it is worth.
Baby Beast 2- 1999 4Runner SR5
Baby Beast -1987 4Runner SR5-Gone, but not forgotten