master cylinder for stock front disc + empi rear discs

[evilC]

If you've got 40mm dual pot calipers to the front and single 36mm to the rear then the front/rear bias will be 2.47:1. That is too much front bias. With standard 944 single sliding pot calipers the front bias is 2.2:1 that can be moderated by the 944 24/19 stepped caliper that gives a 1.38:1 bias with the 944 caliper and 1.55:1 with the VW caliper. The underlining problem is that the rear caliper is only a single sliding unit of limited piston diameter. Change that to something better (say a 2 pot caliper) and your problem will be on the way to solution. Don't get hooked up on fluid volumes as the 19mm piston size in the standard dual cylinder should be more than man enough to move sufficient fluid to take up the slack before pad goes solid - assuming of course that there is no air in the system and the discs/rotors are within tolerence?? Also make sure that the front calipers are plumbed up to the rear m/c piston that is closest to the pedal in all cases.
Also, don't worry about over braking the rear as it is easy to install a brake proportioning valve to limit rear line pressure but just make sure you don't drive it without the valve as the vehicle will swap ends in the first panic stop.

evilC