Grind, Blast, or Coat?
Hopefully your rust situation isn't so dire that you need to cut up your truck. If the rust is superficial and the metal is still in good shape, you can remove the rust and then treat the affected area with paint or a sealer to keep the rust from returning.
Rust removal takes two forms: mechanical or chemical. "Mechanical" means grinding or otherwise abrading the oxidation off of the metal. If you're dealing with just a thin covering of surface rust (which is usually a bright orange), you can sand it off using coarse sandpaper on a sanding board, block, or power sander. For deeper rust or hard-to-reach areas, a stripping disc or cleaning wheel mounted on an electric or pneumatic drill should do the trick.
Heritage Sheet Metal not only makes patch panels for Land Cruisers, it also makes bigger pieces too, like this FJ40 floor, seen at left next to an original '40 floor. Note how Heritage has duplicated all the factory stampings and underside structure. All that was missing were the two gas-tank mount brackets, seen at the top of the floor, which had to be swapped from the gennie piece. | 
Dealing with surface rust can be as easy as grinding it off with a stripping wheel or even some coarse-grit sandpaper on a rotary or dual-action sander. Here, Alberto Gonzalez of Johns Customz & Performance works on oxidation that covered the inside of an old-school door panel. | 
Gonzalez found the rust more stubborn than he expected, so he brushed on Harvey's Gel Rust Remover, a hydrochloric-acid-based rust dissolver. The gel can be left on the metal for minutes or hours, depending on the rust's depth. But with any acid-based rust remover, be sure to monitor its progress, as the chemical will etch or thin the metal if it's left on too long. |
If your rust problem isn't concentrated in one area, you may want to consider having the rusty parts-or your entire truck-media blasted. Notice we didn't say "sand" blasted. There's a variety of different blasting media used on automotive surfaces these days; sand isn't used much anymore except for stripping framerails, axletubes, and other rigid components that won't deform when hit aggressively. For body parts, it's best to use a medium like aluminum oxide or DuPont's StarBlast, which are aggressive enough to cut through rust but won't warp the metal (unless your blaster doesn't know what he's doing). There are even gentler media available, like baking soda and glass beads, but these won't remove rust, just the paint around it.
Professional blasting can be spendy. Job prices vary, but expect a bill in the thousands, not hundreds, of dollars if you're doing an entire vehicle. Plus, you'll need to prep your truck prior to blasting by gutting the interior and removing all the exterior trim and glass. What you'll get back, though, is a thoroughly cleaned truck in essentially virgin sheetmetal. All the rust will be gone, and you can make any necessary sheetmetal repairs on fresh, healthy metal.
Chemical rust treatments take many forms. The one you choose depends on the extent of the rust damage. For example, surface rust can be treated with a rust sealer, like POR-15 or Eastwood's Rust Encapsulator. These products can be applied directly onto the rusted surface, after you've cleaned off any loose oxidation, to form a barrier between the metal and moisture in the environment. These sealers don't get rid of rust, but they prevent any further corrosion.
It sounds strange, but acid-based rust removers are neutralized with water. Any flash rust that forms as a result of the water bath can be removed by wiping it with a little more rust remover, followed by a wipe with a rag soaked in acetone. | 
If the job is big enough, or the rust extensive enough, media blasting can remove oxidation from body panels and leave behind virgin sheetmetal. Just be sure your blaster is using a medium aggressive enough to cut through rust without generating so much heat that it warps the panels. A&M Sandblasting, where this photo was taken, uses DuPont's StarBlast for automotive applications. | 
Look closely at this body mount. See the dimples? That's rust damage left behind after this Cruiser frame was media blasted. The dimples haven't compromised the mount's integrity, however, so TLC went ahead and powdercoated the frame without making a repair. |
The chemical products that remove rust fall into two general types: acid-based or acid-free. The more aggressive of the two are the acid-based solutions. Many, like Naval Jelly or Eastwood's OxiSolv, contain phosphoric acid that eats away at the rust. The problem is they'll also eat away at the base metal if you leave them on too long, and they can damage other materials they come in contact with, including plating. So when using these products, it's best to wipe or brush them on, let them work for a few minutes, then neutralize them (with water, ironically) and assess if you'll need more treatments. Heat affects how quickly these solutions work, so the job will take longer in winter than summer. In fact, Eastwood says you can heat its OxiSolv to 100 degrees F to speed the process even further.
Using water to neutralize acid-based rust removers can cause the formation of what's called flash rust. This thin layer of oxidation can be removed by wiping it with a rag dipped in the remover, followed by a wipe with a rag coated in acetone or a prepaint prep solution, according to Eastwood's John Sloane. "If you're gentle enough with the water rinse you'll leave a minute phosphate coating behind that will keep rust away," Sloane added.
The acid-free removers work on rust using a process called chelating, in which the chemicals bond to the oxidation and lift it away from the metal. This is gentler-and more time consuming-than an acid wash, and it typically requires submerging the rusted part into the solution. According to Sloane, an acid-free rust remover, like Eastwood's Rust Dissolver, is a better choice than an acid-based one "if you're talking about cleaning rust from an area with a pinched seam, such as a door skin wrapped around a door frame. The dissolver won't leave an acid residue behind that could be reactivated [and ruin a fresh paint job] by moisture due to condensation."
Speaking of paint, it's best to cover freshly cleaned sheetmetal with a self-etching primer, as the acid in the etching primer promotes adhesion between the bare metal and subsequent paint layers.
Of course, paint is just the most obvious of the coverings you can apply to your newly rust-free sheetmetal. You could powdercoat the sheetmetal, cover it with a spray-on bedliner, the list goes on. But that's another story.