26 year old 2 master cylinder issues

[Harvey7649]

I have a Neal Brakes Pedals and 2 master cylinder system with a kelsey hayes proportioning valve in the rear brakes line. One master cyl appears to go only to front brakes, and the other goes only to rear brakes. After removing a dragging front caliper and pushing the piston back into the caliper, I seem to have "lost" about 40 to 50% of my braking power. Disc brakes are front and rear. the rear master cylinder offers more resistance than the front one, even with the proportioning valve completely open. Before I start pulling thing apart, I thought I'd ask around and see if anyone has had a similar issue crop up.