Welcome to this area Matt. I was a little confused after reading the title and clicking on your post, as you have an '01-04 tacoma there.
As far as what should you do? So many options. You could forget the bed and go with a flatbed, a fancy adventure trailer bed, or find some fiberglass fenders for all four corners. Depends on what YOU want to do with it. But if you want a replacement bed, one pops up every once in a while on ttora. However, if you plan to build this one, I would recommend boxing the rear frame before you put the new one on. It's so much easier to do without the bed in the way. BTW, any frame damage?
So what are your plans? And does this one have the 2.7 & 5spd?