you can 'clean' the track with some WD-40, but i'd recommend SilGlyde lubricant on track for lubrication. "stays put, water repellant, effective from -20deg F to +400deg F, prevents freezing, harmless to rubber, yada yada yada" good stuff
there are felt covered 'bumpers' in the top of the door panel that press against the glass. they get clogged up with gunk and scratch your window. i don't think they cost too much - you could order new ones or tie a piece of polar fleece around them with a zip tie. there are two per door.