Odds are your front calipers have 2-15/16" (6.77 in^2) or 2-1/2" (4.90 in^2) diameter pistons, for former being the more common of the two for most hot rod type disc brake conversion kits. Your rear Explorer calipers have 1-7/8" diameter pistons. Like you said, the first order of business should be to determine exactly what front calipers you're using.
After that, you need to determine whether you're running power or manual brakes. If power, what type of booster, vacuum or hydro? If vacuum, what size and configuration of booster.
For your reference, the Explorer uses a 1-1/16" bore MC mounted to a dual 9-3/4" diaphragm booster. The front calipers are twin-46mm piston units with ~4.77 square inches of piston area, so just a little smaller than the 2.5" GM units. Assuming a similar pedal ratio, that should at least get you close.
I would think that if you have the larger 2-15/16" GM calipers, a somewhat standard 1-1/8" bore disc/disc master cylinder mounted to a dual-9" diaphragm booster would work quite well. Any smaller of a booster and you'll want to decrease your bore size accordingly. Similarly, if you go manual, a 1" bore MC would probalby be the best fit given your volume/pressure requirements. Lot's of options for MC's either way.
Tobin
KORE3
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