Yes, finally some pics of you doing some work, ha ha, wonderful job man, great pics, documentation and feedback. 11mm bolt you said, those pesky metrics came into the picture, I am so glad my truck is pure standard size nuts and bolts, hee hee
as far as the panels, well, mine were all plastic so I painted them using special vinyl paint, not perfect but turned out ok, (give yours the finger nail scratch test if you can scratch off powdery stuff under your finger nails they are too far gun, if you can't then stain/paint the plastic) yours have fuzz on them (aka much fancier) so donno, maybe steam clean them, or get some new fuzz and have your window guy replace those sections, shouldn't be too difficult looks like a flat piece
Dupli-Color Vinyl and Fabric Paint their Desert Sand Vinyl & Fabric Coating 11 oz. Aerosol looks pretty close
top tip, shop vac the bottom of the inside of the doors, to prevent old hardened rubber and plastic and god knows what else from rattlin' in there and clocking up the bottom drain vents / openings / cracks
also its a good time to take out the door latch/lock mechanism and clean it up real good and re grease it, you'll thank me later it is probably super rusty and crusty in there