Yes I have done chassis painting on many 4runners.
It's quite messy.
So what you have to do it is step1) with a wire brush or grinder get most of the loose rust and surface rust off (the more you get off the better) (make sure you get the top of the chassis as well in all the steps) step2) Use a Rust converter on the remaining rust (any brand will do A liquid version is better but the spray kind will work as well) let that dry it should turn the red colour rust black. step3) Paint it with Tremclad Rust paint (tremclad has a high plastic content so it prevents rust) DO NOT USE THE SPRAY KIND it will NOT last even 2 weeks, Use a paint brush and slap it on as THICK as possible The thicker you put it on the longer it will last, It will be dripping and messy you probably want to put a tarp down. (don't miss any spots otherwise it will start to rust from that spot).
step4) Get the spray kind of rust converter and spray it inside from all the chassis holes Try to cover as much as you can (remember the inside will rust as well)
step5) go to an under coating place and have them shoot BEESWAX inside the chassis (VERY IMPORTANT) and if you opt for it on the exterior as well the beeswax will make the paint last MUCH longer
DO NOT get "undercoating" it will make it rust quicker if it get a hole.
I think I pretty much summed it up. Hope that helps
Some key areas to get the rust out of:
The rear spring coil mounts on top.
The cross bar that the spare tire hangs off of on top.
The Lower Rear control arm attachment joints