Nice work, it looks like you have a solid foundation there. You can POR-15 anything your heart desires. I often apply it all over my hands and legs as well.
The only thing I would be worried about is something like the engine or radiator where it may get hot enough to burn off the POR-15. Many people have applied POR-15 to their axles, frames, etc. The entire floor of my CJ is covered with it, my engine bay, gas tank and skid plate, etc. I really wish they would have had silver POR-15 a while back when I was tearing mine apart because I would have painted the entire tub with that stuff and shot some clear over it!
For the transfer case/transmission skid plate, I would get a breaker bar on those and see if you can get them to move. If the heads break off, you'll just have to drill them out and tap them and use bigger bolts. There are nuts in the frame that they thread into and the nuts are welded in place, so if you break one of those loose (unlikely), all I can say is good luck.