Firstly you would probably be better off using Bmp2000 for your repainting and following the included instructions for repainting AF textures. I say this because Bmp2000 uses full 256 colour BMP as the format so you can use a full range of 256 colours as appropriate for each texture. R8/AF is stuck with a fixed (and limited) 256 colours for every texture of which not all are usable. Following the instructions you end up with proper BMP textures that the model will happily use without any modification (only the filenames are important)
ConvR8 does the best it can with the limited palette but having a different 256 colours for each texture allows for much more flexibility

On the prop spinner. This used to be pretty common. Some areas on the model are not textured but instead just used coloured polygons. One way to change the colours used is with MDLColor (on the Beta page). It will take a bit of trial and error but with it you can change the colour of these non-textured parts in older AF99 and FSDS1 models.