Need help with master cylinder theory/operation, please.

[mickmate]

Hey Dugly excellent report and even better results. Thanks for the update. Does your new master cylinder have two pistons the same size in one cylinder? They call that a tandem master cylinder. That would have two line coming out of it for the fronts and the rears.
You talk about the rears locking first, that's not good. In a panic stop at speed it causes the rear to lock up and try to pass the front end. What you want is a tad less braking on the rear to get what's called a good brake balance. In brake systems with dual master cylinders you can simply change a cylinder size by a 1/16th to increase or reduce the braking on one end as required. That may not be practical with your master cylinder set up so if you simply plumb in an adjustable brake bias valve like this on the rear brake line http://www.summitracing.com/parts/sum-g3905/overview/
Your set up is good for this fix as if the fronts were locking up early you would want to change sizes on masters. You do not want to adjust bias or balance with less braking on the front or put a valve in the front line as they do about 70% of the work stopping due to weight transfer and a gaggle of other considerations. Plumb one of those proportioning or bias valves in to the rear line, have the knob pointing in or up out of harms way and have fun playing with your optimum brake balance.