Firstly check the rubber brake pipes on the wheels (they get old and weak - sometimes they act like balloons) flush all brake fluid with a positive pressure machine, What I think is that the brake fluid was not changed in a long time (or ever) this causes the end of the master cylinder to rust out - in normal condition the pistons never go into that part of the master cylinder. When you bleed brakes on such a cylinder the pistons get there and the seals tear out which then can cause such behaviour in very mild cases.
The only other bit that can cause low pedal is that either the booster actuator is not set with correct clearance or the master cylinder is not from a VTi.