The first issue is caused by internal faces. Navigate inside your model (or turn on xray mode) and you should see faces inside. Delete these - they are caused by extruding edges instead of faces etc. For the other side it may be caused by internal faces again (I can't tell without actually playing with the model) but if not I would just delete the problem face and use the append to polygon tool to create new ones and And what? AND WHAT?! Heh, just kidding, I got the overall idea. I'll give that a go, and if it fails I can always upload the scene file somewhere?