Until recently the only way I had read to correct the fit was done by two different professional builders that said to build a mountain ridge of JB Weld at the front where it connects to the quarter panel, shape it and fill in behind it with bondo. The bondo was of course is subject to cracking because the extensions tend to twist when tightened.
Then I came upon a build on VMF by Klutch titled; 1970 Mach 1 H-Code Build. He said his quarter extension had 1/2" of bondo on it, and he was going to see if he could tweak the pot metal, and maybe get away with just a little bondo. He didn’t elaborate exactly how he did it, so I asked, and here is his response:
Yeah, as is typical, my quarter extensions didn't line up with my quarter panels very well. What I did was to gently clamp each extension into a vice with wooden blocks. Then I very carefully bent the metal in the direction I wanted it to go. I just did it instinctively. There was a big pucker factor because I was the afraid the pot metal would crack or even break. Surprisingly, that didn't happen. It took many attempts at bending and test fitting each quarter extension until, finally, I got it to where it lined up quite nicely. It was one of those situations where persistence paid off.
If you want to try this, I can't guarantee your quarter extensions won't crack or break, but it sure worked well for me. Good luck and have fun!