All that's left of the original car is the rockers and the cowl. He replaced the floors, crossmembers, front rails, etc. And some some of that stuff wasn't even there to begin with, like the radiator support.
So as long as he's basing all of his locations off the factory measurements he should be ok. I'd start mocking up body fits as soon as possible and before I probably finished welding everything else, but you have to start from the rails and work out. The published factory dimensions are pretty much all based off the frame rail locations, you put those where you need them and then make sure you don't pull them out of whack as you add the rest of the structure.
