I'm sorta new to this forum, but here's what I did to repair some rust recently.
Here's a common site, a lead acid battery leaking for years and years, seeping acid onto the frame below.
1 bottle Naval Jelly Rust Remover $6.00 (local hardware store)
1 Can Spray-On Rust Converter $5.50 (local auto parts store) *sealer/primer will also work
1 paint brush $3.00 (local hardware store)
1 can Plasti-Dip $5.00 (local hardware store)
3 Stainless bolts, Nylon Sleeves, and Stainless washers $4.00 local hardware store.
I removed the battery tray with some care. The three bolts that held it in place were rusted into the holes, a good soak with penetrating oil may be needed. The underside of the bolts can be accessed through the inner fender-well. The Battery tray is fiber-glass with metal sleeve inserts to center it, held in place by shouldered bolts. There is a drain hole in the bottom of the tray that drains almost dead center on the frame rail. Mine was full of dirt and build up and the tray had been over-flowing whatever moisture built up in it, washing battery corrosion onto the frame. I didn't try to pull the metal spacers out of the battery tray holes, just gave them a good coating of sealer. This is also the only way to remove the bolts that hold the cross member to the frame on the drivers side, so it's a good idea to make sure those holes are clean and the bolts are in good condition. I'm doing this during engine removal/replacement, but you could remove cross member bolts one at a time and treat if needed with some careful jacking and support of the cross member and frame.
After removing the tray and giving everything a good dust off, all rusty and/or exposed metal got a coat of naval jelly, follow the directions on the container, but basically you want to lay it on fairly thick with the brush and use the brush/bristles to push it into every nook and cranny you can. I also used this process on the battery hold down and J-Bolt and the clip that holds the J-Bolt to the battery tray, then used a few coats of primer and the Plasti-Dip on the battery hold down and J-bolt and clip to seal them up good.
After the Naval Jelly treatment I used a metal brush, and scotch bright pads to remove the fine bits and prep the surface. I had some left over scotch-bright buffs and a dremel from porting and polishing. Power tools will speed thing along, but are by no means required for this job. I also used Acetone to clean and prep for sealer spray.
The sealer goes on thick and clear like jellly and there is NO little ball in the can to rattle so don't beat the can trying to get it to rattle. It's basically like a clear coat. Also, it's important to follow the directions on the can, it requires some set time, and will turn the exposed metal to black as it goes through the oxidation process. I let mine sit over night. Don't worry about getting over spray on painted areas, the stuff stays clear unless it contacts bare metal or rust. Be sure to get the underside of the frame too!