Only way to get rid of rust is to cut it out and replace it. If the spots are small you can just cut out the rust and weld in patches, but if it's a significant area of the rails it's just easier to replace the whole thing. Pretty much everything on these cars is spot welded, so, you can replace everything with a spot weld cutter, a MIG and new pieces. It's actually not all that hard, the worst part is setting everything up level and square. More tedious than anything, lots of measurements to make sure everything ends up where it's supposed to be and you don't end up with a car going down the road sideways.
If you plate or box over the rusty spots all you're doing is buying some time, the rust will eat the new plate or boxing faster than the original stuff, you're just trapping it in a bunch of layers.
Replacing a rail is easier than welding in a cage and all that reinforcing stuff. And less expensive in a lot of cases too.
