do whatever you can to find where it needs to be shaved and use a long block and 80-180. I'm doing something like that on my Mustang for the fender/quarter extensions. I walk up to the car and hold it in place where it's supposed to be, mark where it's touching and not allowing other places to touch, run to the vise which has my file in it, file for a couple minutes, and then run back to the car and re-check fit. The fender extension was so bad I questioned whether or not it was even for a 65, but after some filing and hitting it with a rubber mallet here and there it fits perfect.
Emphasis on using a block.