I had the same problem you described and I tried everything you and mtn_jake have tried. Like yours all the measurements were correct on mine, and I thought maybe I had frame damage. My fix was to use a Dremel with a small cutoff wheel and cut a slot on the framerail bottom at the interference point, then two vertical slots at the ends of my first slot. I then pushed this steel flap that I made into the framerail and welded the seams shut. This created a solid clearance notch and plenty of room for that header tube. Try thinking of an envelope flap beinging inserted into the envelope for a second. This worked for me on a '72 Swinger but you may not want to do this on a rare or expensive car though. This would be extremely hard for 99.99% of Mopar folks to notice when the welds are smoothed and painted.
Bob