You could run the 99-04 SuperDuty master cylinder...aluminum body, plastic reservoir, screw-on cap, 1.375" bore. It came with ~13" rotors, however the piston areas of the calipers are actually smaller than what you're running at 7.06 sq in for the front and 4.98 sq in for the rear calipers.
Your setup with the T-bird/LTD front calipers has about 7.5 square inches of piston area up front and 6.77 square inches in the rear. Given your wheelbase, smaller rear calipers would really work a lot better as you can only do so much with a proportioning valve (assuming you have one), but the larger bore SD master cylinder should make your pedal higher and firmer and make your brakes less senstive. The greater the effort needed at the pedal to achieve lockup, the better your brake control and modulation at the pedal.
Anything larger than the 1" bore unit that you're running now should be an improvement in the pedal feel.
Tobin