Here's my two cents...
I have the same problems. On my passenger side, there's a small gouge near the top of the window. (I have a 99 si BTW) On the drivers side, in the same area, it seems a small animal made a 3 line scratch about 4 inches long sort of like a musical staff. For the gouge, i was thinking that if i could get some sort of vinyl plasticky touch up stuff and apply it over the blemish. Then, maybe with putty or something, make a mold of the pattern of the door trim and then apply it over the touch up liquid to match the rest of it. You could do the same for the other side. Hope my idea helps.
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1999 FBP Civic Si: B18C1, B16 Tranny, Exedy Stage 1 Clutch, ACT lite flywheel, Apex'i WS Exhaust, NGK Irridiums, Eibach Pro-Kits
Audio (nothing crazy):Premier DEH-P780MP, Pioneer speakers all around, Pioneer 12" sub, MTX Amp
AIM: babygrand103