Just because your XR does not show any obviously visible rust, not assume it is rust free. The lower body cladding, and particularily the rocker panel, can hide rust formation for years before it becomes visible. Any by then, it's probably too late.
The cladding can easily be removed by pulling the strips out and then drilling the rivets out. Same goes for the plastic rocker panel cover which is riveted to the door threshold and snaps into the unibody seam below. This is where the biggest problem area is, especially on the driver's side which is subjected to more winter salt, sand, and slop. Complete perforation is common here, and here's my treatment plan regardless of what you find.
1) Completely scrub the area of all dirt and rust scale.
2) If rust is present, get the wire wheel and/or grinder out and remove the "Cancer" back to bare metal.
3) Paint entire area with Wurth Rust Guard or POR-15. If you went through the floor, hit it from the top side too.
4) Top-coat with good quality enamel - I used Masury Rust-No-More
5) Any small holes can be filled with silicone caulk; big holes will require Bondo or welding (preferred).
6) Re-install cladding after thorough cleaning.
Rather than re-rivet the panels back on, I took a different
(somewhat controversial) approach. For all the vertically oriented
panels, I used a double-headed door panel retainer (Part# WF 40144)
along with a healthy dab of clear silicone caulk on each one.
The outer head had to be trimmed somewhat to fit into the cladding
holes, and the holes in the body had to be enlarged to 1/4"
(just be sure to repaint the bare metal of the fresh holes). For
the rocker panel cover, I used a black 1/4" push nail retainer
(Part# WF 41635), along with the silicone caulk. Since this approach
is "less permanent" than the factory riveted approach,
I'm hoping I'll be more inclined to do a bi-annual removal and
cleaning. I also installed all new 1/8" thick by 3/4"
wide foam padding around the inside of the cladding, in the factory
original location. I have a bunch of this left over, if someone
is interested in purchasing the remaining portion of the roll.
Plastic retainers were ordered from Harry's Automotive Warehouse (800) 239-8149.
There are five drain holes along the bottom seam
The purpose of the vents in the bottom of the cladding is to
help let any water or water vapor out. The moisture is what they
try to stop in car design. Yes, it does collect crap but the water
is what causes the rusting problem. One other thing that you may
want to consider if you have to do rust work is to avoid bondo
if possible. Bondo is made of polyester resin and styrene monomer.
Polyester absorbs moisture. If Bondo isn't completely blocked
off from all moisture it will absorb moisture and accelerate the
rusting and blistering that you just fixed. The best alternative
is to use an Epoxy primer on all the bare metal and put the Bondo
on top of that. Each company's products are different so you have
to do a little research to do this correctly but it's the ultimate
You must take the mirror off to remove the "belt" weather-strip (around the glass). I you don't, you risk bending this part - a REAL no-no. The one-way reed-valves at the door bottom are probably falling apart. I haven't checked, but they may be Ford or German car generic. The rear glass run is often loose - makes a squeak over bumps - left ear area. The very rear lower corner of the door doesn't get rust spray from the factory - check VERY carefully for any bubbles in this area. Even without dirt buildup, rust is possible.
Check under the front of the spare tire for rust. Either the design or the manufacturing left an area that does not have good corrosion protection which leads to failure. I just fixed mine. It's an area where there is a beam contacting the body shell which rusts quietly.