Check out the poor job somone had done on the door sill replacment (I think most of you may know them as rockers?). They hacked off the old sill but left the old sill flanges attached to the body! This made the sill stick out about 3 to 4 mm from the rest of the body line!
I took the complete thing off and removed the original flanges. I also made a new top plate as the old one had rust pitting in it.