There are holes in the body and they line up vertically (front to back) with the holes in the sill plate. The problem is they do not line up horizontally (side to side). They are too close to the outside of the car. I don't think the body shop covered them because they did not do any work on this part of the car. I could try bending the plates a little, I was just worried I would destroy them.

 

Take a picture and post it. Thats the only thing I can think of now. Show us what you mean.

 

I just did this last week. I got the stainless steel ones from NPD and while the quality was fantastic I had a b|tch of a time getting them to fit. Not because of the scuff plate but due to my new seat risers. Once that issue was corrected I found that inside screw holes were a pain to get lined up. Wasn't easy but I got most to line up except for 2 inside holes. Rather then cut, drill, modify the scuff plates I decided to simply drill the 2 new holes into the sill to line up with the scuff plates.

A couple small holes there IMO is not a big deal even on a mostly original car. I'd rather do that then cut/drill new holes in the scuff plate.

 

I have the same sill plates that you got. I just had to work them a little bit to make them fit. You may find that having 2-3 ice picks will be helpful.