James,
I usually have to play around with the headers for quite awhile to make them fit. It usually involves creative cutting and welding.
Keith has an excellent point, why not buy a set of Kirkham headers. They come out of the box fully welded and fitted, and they do fit! You should be able to use your Shelby sourced sidepipes, or the Kirkhams if you wish. The Kirkham sidepipes look original, but are much louder than the Shelby pipes.