Since the videos were recorded, I have fixed the missing colors in Star Wars (lasers, HUD, targeting reticles, etc.) Harley Davidson and Ocean Hunter are showing some 3D but they crash because of unusually large display lists. I'm not sure what's going on.
Despite having spent the last two days looking at it, there has not been any progress on the flickering, bad polygons in Sega Rally 2 or remaining issues with material colors, unfortunately. I think I'll move on to other aspects of the emulator next weekend. All the easy stuff has been figured out and what remains is quite tricky.