I don't think the problem is the frame rails being out of square, I think it's the driver's side radiator support side panel that's installed incorrectly. I agree with cudascott that you'll need to drill out the spot welds and reposition that panel. It pretty clearly is installed too far toward the center of the car.
Here's a pic of my 63 at the inside left front corner of the engine compartment. Hard to get a good angle with the battery and so forth in the way, but I think it's clear that my side panel is installed closer to the frame rail than yours.
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