Rust on the corners

[Vulcan]

I have some small rust issues on the sides of my 2000 Ranger. It's in 4 places. Between the wheel-wells and the door on the bottom (both sides) and at the back of the cab on the bottom where the suicide doors are (both sides). Each areas spans a width of about 4 inches before meeting a seam. The problem is complicated, and perhaps caused, by a clear covering applied over the paint. This has caused the area to blister and then rust where the water leaks out. It looks as if it is only surface rust at this point.
My questions are:
1. What is a cheap, serviceable way of fix this? Other help forums seem to want you to buy expensive tools and have access to a paint booth. I just want to fix it so it keeps the elements off the body.
2. Should I replace the clear covering and if so what is it called?

I am trying to nip this stuff in the bud the best I can. I really like my truck and don't want to see it rust out around me as the drive-train remains reliable for miles to come. Thanks in advance.

 

[whale]

Unfortunately, once rust is there, the roots of cancer have taken hold. It's hard to arrest unless you get past the roots.

Clear covering, I think, is called clear coat.

Will

 

[chrwilkins30]

well if it is surface rust. i would sand it down apply por15 and then bed liner the bottom of the whole truck. but thats just me.

 

[lone-wolf]

grind down to good metal, paint.
That is the quick and dirty solution.

 

[Vulcan]

My bad about the "clear covering". I thought that there was a plastic applique on top of one of the areas that was bubbling but on further review it's just paint.
I think I will go the bed-liner route once I get everything sanded and cleaned up.
If anyone is interested, I believe the cause of the rust was dirt and sand that had accumulated in the corners at the back of the cab. I had enough built up over the years to form my own fossil record. Might be worth taking ten minutes and cleaning out those under chassis recesses.