Shaun,
How well dos it line up with the body lines and gaps in between the door and the rear pillar post and the front fender?
If the door is aligned correctly/perfectly on the pillar side, the bottom, and the top of the door shell and there is no gap between the door and where the fender is (when properly aligned) then you're goign to have to carefully lift up the folded edge and refold it.
If there is the correct gap between the door shell and the fender then you're either ahve to leave the gap and seal it with caulk, or but weld an extension onto the door frame.
On the door shell for my 72 (even though it was a true NOS piece) there was a slight gap between the door shell and the corner bodyline that i could not get straight. This was partly due to the fact that the door was hit straight on there and the metal is super thick and i couln't bend/ form it much. So i used a lil bit of caulk to fill the very small gap (less than the size of a dime).
So my advice is to double check all your alignments, top-bottom, front and back. Also make sure you double check the all the body lines, several times. Post or email me more picts of the body alignment if you want.
PS for the padding get some foam insulation pads from Home Depot or Lowes. Also por-15/rust preventative coat the inner door and skins, then coat them with a sound deadener or spray on rubber under coating.
If you haven't seen my write-up (which i think you have) here is the link:
http://www.desertmustangs.com/1972coupe/Door_skin_repair/72-Door-skin.htm