3/4" master cylinder?

If the pressure testing was with the caliper installed on the knuckle, you probably have some air being compressed at the adapter. Caliper pressure can be checked off the knuckle with the rotor or block of wood between the pads and the bleeder/gauge not on top. Could also try loosening the gauge from the adapter so it leaks, then tighten. It sounds like you just need to go with a smaller bore master or a booster or a custom offset push rod (like fords) for a pedal modded to a higher ratio (raised attachment).