Your problem isn't too uncommon, Davey. I can remember several stovebolt pickups I've driven that had an annoying "SQUEEEEEEEKKKKK" when the clutch pedal was operated because the pedal shaft was dragging on the floorboard. The quick fix was to open up the hole a little if the bushings on the pivot were in good shape. Since one pedal is off in one direction, and the other is different, that pretty much lets out misalignment of the pivot shaft. I suspect the holes through the floor of the new cab might be cut a little differently than the original. Just hog 'em out a little! Isn't there supposed to be a pretty good-sized rubber washer on the bottom that serves as a dust seal? If not, cut a donut-shaped piece of the sidewall of an old tire that's a snug fit on the pedal shaft and covers the hole from the bottom to seal out dust, and prevent a cold air leak in the wintertime. Good luck!
Jerry