brake issues, out of ideas...

It almost sounds like the residual pressure valve isn't installed in the master cylinder you are buying or it isn't working. You might want to check the application of the master cylinder you bought and see whether or not it has a residual pressure valve in it.

The residual pressure valve basically is a check valve and forces the system to keep 10lbs (or so) of pressure on the brakes. If you don't have that pressure on the brakes, then the springs in the drums (attached to the shoes) will squeeze the shoes inward and drive the fluid back in to the master cylinder. The result is that you have to pump the brakes up. You are forcing the fluid back to the wheel cylinder and re-expanding the brake shoes.