I just did this about a month ago because it was really starting to bother me. I'll get pictures up next week but this is what I did after reading and reading up on rust prevention. I decided I wanted something that was spray on instead of paint on, bc brushing seems too messy.
1. Took my 4runner to a manual car wash and washed the underside, I think I spent $5 in quarters. I just used water.
2. Waited for it to dry, then the next day removed the spare tire.
3. Got underneath the truck with a cordless drill and a wire brush. My was pretty bad so I had a lot of stuff come flying off. Wear long sleeves, eye protection and a mask!! I think I spent about 2 hours wire brushing everything I could get my drill into.
4. Then I briefly wiped everything down acetone, I got pretty lazy with this part bc I really wanted to start spraying.
5. I ended up using 3 cans of Eastwood Internal Frame Coating and tried to coat the inside of the frame as best I could. It comes with a long tube/hose so you can get it pretty deep inside. Wear eye protection and a mask, this stuff seems pretty toxic! One area I was noticing that saw more rust then normal was rear trailing arm connection point to the frame. I guess since it sticks out and is open, salt and water can build up in this area. Note to self remember to wash this area off more often.
Amazon.com: Internal Frame Coating Rust Prevention w/Spray Nozzle: Automotive
6. Then I used 2 cans (maybe 3 I forget) of Eastwood Rust Encapsulator Paint - Black Aerosol. I only did one coat of this, but it seem to cover pretty well. The first can was fun bc you're covering everything up, the second can (or the rest) was just tedious. I think this part took me around 2 hours.
Eastwood Rust Encapsulator Paint - Black Aerosol 15 oz : Amazon.com : Automotive
7. Then I let it sit for 24 hours to dry.
8. Next day I used 1.5 cans of Eastwood Extreme Chassis Black Paint Satin Aerosol 14oz. This was a slight pain bc it was hard to paint black on black primer. I wish there was a different color for the primer. I think this took less than 2 hours. Remember to wear long sleeves, eye protection, a mask and gloves!! this stuff is hard to get off. Always wear latex gloves anytime you paint anything, that's what I've learned.
Amazon.com: Eastwood Extreme Chassis Black Paint Satin Aerosol 14oz: Automotive
I never removed a wheel, but I bet I could have done a better job with the front wheels off. Actually I had to fix a squeaking coming from my front driver side brakes (my rusted brake shields were touching my rotors) and I ended up spraying encapsulator in that area.
If I could go back I would have added one step before the encapsulator... Eastwood Rust Converter Aerosol Stop & Prevent Rust.
Eastwood Rust Converter Aerosol Stop & Prevent Rust : Amazon.com : Automotive
But now I'm not embarrassed when people look at the 4runner. It actually looks pretty good. I forgot to check but when I jacked up the frame I was wondering if the paint would chip on not. I dont think it did.
-------------
Too much text with out pictures is boring. Sorry I'll get some up soon.