Low brake pedal - please help

[Mastiff]

I showed the MX-3 ('93, 4 cylinder) last week (you have to show it at an aproved garage every other year to keep your plates here), and the mechanic said that the brake pedal was to low. I have a friend who's very good at such stuff, and he had overhauled the rear breaks one week prior to this. New seals, pads, shims, fluid (which of course cover the whole system), the works. I know about the pretty weird hand brake system, which screws the pistons towards the pads, and there does not seem to be anything wronge there. When he opened the system up again, he saw that one pump of the lever that the hand brake cable connects to, will move the piston all the way out when it's screwed in, and it won't go back. Still the pedal is to low. Does anybody have a good idea here? I'd really appreciate it!