if a surface is supposed to be contiguous (all one piece) make sure there are no splits in that part of the model. Sometimes Remove Doubles doesn’t clean these up because the vertices aren’t close enough together for the default Merge Distance (see Tools on the right hand side of the 3D View). If you adjust the Merge Distance after clicking Remove Doubles, you can clean up more of the gaps this way. Keep an eye on your mesh, though. If you go too high with this value, the mesh starts to eat itself.