There is one more thing. You said the master cyl. is new. If this has a brake booster[hydrovac] that is mounted on the frame [not part of the master cyl. assy.] then when they made the master cyl. they propably put in the residual check valve. This valve will keep a small amount of pressure in the brake line going to the brake booster. That would be why it is not letting all the fluid return from the brakes. You can check this by removing the master cyl. and dissasembling it. Look for this residual check valve on the end of the return spring. If it is there, just remove it and put it back together.
