TDeacon;
I have not look at the p51b skin yet so I can't answer your questions precisely but here you go:
1) There is something known as "UVW mapping" that "maps" where the pixels of the skin goes on the 3D model. It is possible that the outer gear door and tire share the same map location – HTC would have to fix this. It is also possible that the tire is drawn too large on the skin – something you can fix. To determine which case applies, try "painting" the entire gear door gray and see if any gray appears on the tire. If it does, then they share the same location. If that were the case, I would recommend leaving the gray on the tire since it is only visible when the gear is down. When I do skins, the default skins is used only as a "suggestion" of the UVW mapping. I go through and define where each piece of the 3D model is located on the skin and how each piece is linked together.
2) The "dented" fuselage in not cause by your system. It is part of the model.
3) I can't see the triangles in your image, my monitor is too dark, but this is usually caused by the UVW mapping for those two triangles. They could be mapped to some obscure location on the skin.
4) Again, this sounds like a problem with the mapping and there isn't much you can do about it. Just for your info, the p51d only has a single prop blade on the skin that gets mapped to both the front and back of the prop. I elected not to put any markings on the blades since you would most like be looking at the blades from the cockpit.
Best of luck with the skin.