I also recently noticed the 'compost pile' accumulation in the door-side wheelwells of my '89 3-door, probably from parking under a tree for years. Mine was so thick that after I stopped whining I had to remove the plastic guard and hose it out.
Sorry to say but for me, anything less than a rustectomy will eventually come back. For the bubbly type of surface body cancer, I have done anything from grinding down to bare metal with metal bits, wire brushes, nylon brushes, sanding discs, etc. The rust pits are the hardest to grind. To eat away what the grinding doesn't, I use 'Metal Treat' which is a greenish phosphoric acid solution, diluted 7:1, that does a fine job of chemically converting the rust to a paintable surface and prevents flash rust from forming. Its kind of nasty stuff but it works. Use gloves. Then prime and paint. I usually spend 10x grinding and 1x treating. If you can't get to bare metal this time don't worry, you'll get to repeat it all again next year

For the kind of cancer that is so advanced that it has left just rusty metal and holes, the above will not work by itself. Use fiberglass epoxy and move to Arizona.
hope this helps, 89Ru