Auto Metal Direct Fitment Issues?

Yessir. Measure the chassis, check it vs the specs, and then start the process of lining everything up. I honestly wouldn't be totally surprised if the major chassis components measure out ok, or close to it. Even when they do a lot of fitting is sometimes needed to get everything lined up.

The door fit is going to be the big test. But even there, you have to make sure the door is right too, you don't want to be fitting the rocker to a door that's sagging on worn out hinges. That's why replacing the rockers, quarters and floors is such a big deal. It's not that hard to drill out the spot welds, and really it's not even that hard to weld everything back together. It's getting everything to line up. The more parts that get replaced, the less reference points you have. With your car needing rockers, floors, and quarters you pretty much lose most of your reference points for the body. That's a ton of moving parts. The rocker is a big deal, the rocker placement will effect the locations of the quarter and the fender. And the door has to line up with all three. And then the floor still has to fit to the rocker too. Never mind that the fender placement also effects the hood gap, and the quarter placement effects the trunk lid fit, bumper gaps, heck even the rear window.

Basically, to do a rocker, floor and quarter you have to juggle every single body gap on that entire side of the car. And that's why it costs so much to do panel replacements, and why it gets exponentially more expensive as you add panels.
Thanks for all the info! Hopefully the wallet won't be hurt too much. I'll give the specs to the frame shop and try and see if we can determine the best way to remedy the fitment problems from there.