You may need to shim the BODY on the frame! I don't know that particular car but this was very common with early V8 Ford roadsters, the sill plate is not very strong and shimming the cowl to bring up the back of the doors is the norm. Think about it, they fit before the frame swap.........the hinges didn't somehow change, it is the fit of the body to the frame that changed.
Now, can you fix it if it's just minor thru the hinges, sure. But that may not be what you should be doing, that I can't tell from this side of the computer.
Brian