On the Tacomas (95/96) the original bed is bolted at 4 points. I've reused the factory bolts
and mounted my aluminum frame to those. (it was seven 2x2 tube crossmembers bolted to two 2x5 tube extrusions which were then bolted to the four factory bolt points.
In my next build, I am reversing the crossmember and extrusions that are inline with the chassi, as it will give me an extra two inch rise for less material (In other words, I am bolting two 2x2 crossmembers using the four factory points, THEN laying the 2x5 tube on top of that..then I will lay my primary crossmembers above that (probably gonna go w 1x1 for those as my boxes are pretty light)
In the field...er, sandbox.
May I suggest you check out Di-bond, Maxmetal, alumacorr, Alupanel....They are all pretty much the same thing..just different name brands.. aluminum sheet with a plastic core.. (Ask your local sign guy if he can sell you some sheets (3 and 6mm thick.. .125" and .25"equivalent. They won't rot..You will probably want to use plywood or some such "screw holding" material on the inside if you are doing any shelves,storage,etc..but at least then the wood is separate from the outside and as long as you do a good seal job, should not get wet/rot.
Looking forward to seeing more of your build!