Good that you caught that wood rot before it got too far. A lot of people fix it with a special epoxy that works wet. You probably can do it without a problem but most important is to find out where the water came in. Possibles are roof leaks, upper wall seam caulk leaks, screw holes (like those self tappers you mentioned.) Search on delamination to get a lot of info. Much of it may not apply but the cure is probably the same.
My Beltline trim was held on with double faced tape and I replaced it with new stuff that had tape with it but you can probably use one of the 3M tapes to do it.
Roof seal with a self leveling caulk like Dicor is critical in preventing leaks and rot. Do not use silicone. Side seams are equally important.
I removed my graphics with a heat gun on low and a plastic scraper (very carefully.) When that is done you will see the original color beneath where sun has not faded it. When you say buffed do you mean with compound? If so then do it before the new graphics are added. Then polish (wax) a week or so later to let the new stuff bond. I went to a boat graphics shop and designed a huge blue wave breaking over a desert island with a palm on it and the RV's name "Tsunami" Nobody else has that logo/ graphic. It got the name because once it gets going it's hard to stop. I surf.
33' 2008 National Tropical on a Freightliner chassis.RVM#189