Well, I think I may have found a solution. Here is my thought process:
Problem:
In a single circuit system the wheel cylinders all expect to be at the same PSI when braking. The front to rear brake balance was set by carefully chosing wheel cylinder sizes.
If you convert to a dual circuit system, uneven braking could occur because the front and rear brakes use very different volumes of fluid, and would build pressure at different rates.
Solution:
Split the brakes up diagonally. By doing it this way each circuit should require the same volume of fluid, and all should build up pressure like they would normally in a single circuit system.
It would probably also be safer to split them up diagonally so I would never lose both (huge) rear brakes at the same time.
The key to this plan is just making sure that both chambers in the master cylinder are sized the same. I guess this was common with drum/drum dual circuit master cylinders, so hopefully it will not be an issue.
I will probably just pick up a refurbished master cylinder for $33 (R12700, it should work with a firewall vacuum booster I have on hand), and see what happens.
I will also pick up two brake pressure gauges so I can see how well this all works.