I bet you have a "Corvette" 1 1/8" bore master cylinder. That would explain the reversed ports, hard pedal, low line pressure and decreased braking performance.

All else being equal, a smaller bore master cylinder increases your mechanical advantage at the pedal. The result is a longer, lighter pedal stroke and increased clamping force at the calipers.

BTW, post '72 power brake A-bodies were originally equipped with a 15/16" bore master.