Auto Metal Direct Fitment Issues?

Even in the factory service manuals right below the measurements I posted above it says the chassis measurements can be off by a 1/4". And that's the structural measurements, not the body. If the chassis can be off by a 1/4", you can figure the body can be out even more than that.
My friend told me something similar about his Super Bee when he was replacing the quarter panels. I'm not really seeing any other solutions than measuring the chassis again and referencing it with the frame print, then massaging and modifying the new metal to fit using pieces from the old panels. Which, unfortunately, is probably gonna get pretty costly.