After a couple pages of math and learning about braking systems and how they actually work I think I found a solution for guys with big brakes. Richard figured out that the 99-04 booster has 47% more surface area in the dual diaphragm booster. Dodge for some reason up sized the master to a bigger bore. That yields more volume but less pressure. Most guys who I have talked to with big brakes who are honest with themselves are not really impressed, somewhat stiff pedal and marginally better braking.
After doing the calculations based on caliper piston size the master cylinder/booster setup is mismatched terribly for bigger brakes. While they might work it isn't working correctly.
The guy at wilwood was nice enough to spend some time with me on the phone and he was even going in circles for a minute. But he recommended a 7/8 bore master with manual braking master and a 1" with the given surface area of the 2000 booster.
Another consideration is our approximately 3.5:1 pedal ratio.
I have changed some things out on my setup and will update this thread good or bad.