If the rust is that bad enough to have eaten through the sheetmetal, you should probably cut your losses now. Sell the truck for what you can and purchase a relatively rust free newer Runner. With the new runner I would use a quality rust stopping undercoating, something like POR15, or one of the higher quality D-I-Y bed coatings, or a pay to have Line-X sprayed on it. Line-X is going to be more expensive the the D-I-Y job, but it should be a one time deal.

More than tread lightly. Leave it like you were never there, nor anyone else.
'90 X-cab 4.88's 33 BFG AT's, rr ARB, Headers, Ignition upgrade, cold air induction.
'91 X-cab 5.29's 315's BFG MT's, rr ARB, custom bumper and flatbed