This is something I've been over many times.
First on the spare location - I don't have anything there currently but for some time I've been doing a mental exercise of adding a water tank and pump there. With the rear heat you already have engine coolant plumbed to the rear of the rig - it would be easy to tie that to a simple heat exchanger in a water tank. boom: hot water. The catch is finding a tank the right size. There are tons of ridged poly pre-made tanks out there and you can get kits to add your own ports where you need them, but it's still going to be tough to get something the right size. Since you'd have to fab up a skid plate and mounting anyway, I think I'd just make a metal box, open on the top, and use a bladder tank. They are a little more expensive than poly and may pose an issue with the heat exchanger but would offer maximum volume since they will conform to your available size.
For a pump, the smallest 12v marine pump would be more than enough. You don't want a high volume pump anyway since you'll be trying to save water so even the smallest will do the job. In my case I already have a 6 ga power wire run to a disty block in the cubby on the back/ drivers side for future upgrades so power would be easy. For the outlet, a simple RV type external plug-in shower would work. No need for a mixer since you won't be drawing from a separate hot and cold supply. The filler port would be the hardest part. I think in my case I would use a generic boat filler (boats are what I do, so naturally that's what I think of first) and mount it into the top of my rear bumper. With a stock bumper I don't know if you'd have space or want to cut into it, so you'd have to figure out where you want to put the filler so it can gravity feed to the tank. You'll also need to run a vent line, but that's generally 1/2" and shouldn't be hard to find a space for.
On to the mufflers. The 'turtle' - i.e. the big center resonator, is a low point and commonly bashed up. The up-stream center muffler also tends to take a beating, as do the two pipes that pass on either side of the diff. Some people have claimed they cut the exhaust off after the first center muffler (between it and the 'turtle') and put on turn-downs with no ill effects. "you can't even hear a difference" they say. Well, let's just say Your Mileage May Vary.
I tried it last year. First of all, you most definitely CAN hear a difference. Not so much in the driveway or even on the trail, but on the highway it drones and is pretty annoying. It wouldn't be so bad in a beater trail rig, but these are still nice trucks. Maybe if you're not particularly attuned to your truck, or you always blast the stereo it wouldn't bother you. But I got past the willingness to put up with crappy droning exhaust about 25 years ago.
The bigger problem however was the heat. The turn downs didn't do a good job of getting the hot exhaust gasses out from under the truck. This led to me melting the plastic air intake line to my compressor where it passes over the diff (it is behind a heat shield but that wasn't enough). That let to a suspension failure when the compressor couldn't draw in any air because it sucked the softened plastic pipe closed. I replaced that pipe and wrapped it in heat shield tape but it still happened again. This only occurred on 90*+ days when running very slow/idling on the trail, not at street speeds. Makes sense when you stop and think about it.
I ended up putting my exhaust back on. it's pretty bashed up, plus I've cut it apart and now have it clamped back together, so I'm about to swap it for another stock system I have waiting for me up at British Recyclers. (actually hoped to pick it up today but Justin was closed for the holiday) In short, I don't recommend cutting the exhaust like that despite what others say they've done.
I believe MagnaFlow offers a cat-back system for these trucks but haven't looked into it. That may be a way to get rid of the turtle at least, but I'm betting they still route the pipes the same way past the diff since there really isn't much other room there. And honestly I like the truck being quiet - loud doesn't suit this sort of vehicle in my opinion.