I've shared my experience with rust on the forums before but I'd like to bring up so key factors about this rust problem. Rust needs to be eliminated 100%, which is near impossible. However, if you can get your 4runner frames down to bare metal and coat it properly at the onset of rust then this whole rotting through issue can be avoided.
After discovering shocking amounts of scaly rust on my frame, axle, and suspension linkage I did TONS of research last summer to fix the problem. First off, the spray can crap from the auto parts store does NOTHING! I sprayed over the rust for 2 years; its a waste of time and can be more detrimental.
Here's what I did:
1. Frame, rear axle and everything around it was sand blasted to clean, bare metal.
2. On a warm, sunny day spray down the new metal with soap and water to clean the surface as well as possible, then dry with fans or air hose to speed up the drying process so you can start painting same day before flash rust occurs.
3. Spray on "Rustbullet" stage one, the gray/silver base coat ($50/pint). Apply coat one, let dry, apply coat two which fills in all the pin holes from the first coat. The stuff is THICK. I used about 10 paint brushes, if I could go back I would pay someone to spray it on.
4. Apply the Rustbullet black top coat.
5. Run your truck through the car wash every week in the winter! Depending on where your hot water heater is in your house, you can run a hose out to the drive way and spray down the frame once a week. You can also spray the inside of your frame rails with grease or used motor oil as well as your entire undercarriage.
POR 15 works well too, but more so if you are trying to paint over rust, as POR stands for. For clean metal I believe Rustbullet works better. Even after all that work I did, surface rust does come back in small insignificant forms, but staying on top of it is the key. Rust is oxidation thus it has to be choked out and encapsulated to stop the spreading. It is unbelievable these frames rust so badly but I realized over the last couple winters that bad damage is some what avoidable.