i'm looking at buying a '88 4runner. The guy selling it said it does have the usual rust around the fenders, maybe 6 inches around each fender. What is a good way to stop, and then fix these types of rust spots? Is there a website to buy stock paint for these old 4runners to use as a touch up?

Touch up wont match really due to fade, you will need pro help.

Rust, really cut and paste is the best for remove and replace. Means cut off the rust and replace with a new panel. There are some paints/coatings you can use. Look under restoration paints on the internet.