There is a lot of debate back and forth on the advantages / disadvantages of MIL-5606 vs DOT-4 brake fluid. The vast majority of light aircraft use MIL-5606 fluid for the brake system. 5606 is mineral-based hydralic fluid which has a fairly low flash point. There are a number of brake fires (a couple in RVs) that were helped along by the flamability of 5606.
I have decided to convery my brake system over to use DOT-3/4 automotive brake fluid which has far better performance. The downside - all the seals in the brake system and the flexible hoses provided in the kit are not compatable with DOT-3/4. Luckily, another builder already put together and o-ring replacement kit for cheap.
Another problem is that DOT fluid absorbs moisture so it has to be in a sealed system. The Vans brake reservior is vented to the atmosphere, so that won't do. I already found a very good replacement and will have more on that later (once I buy it).
Back to work done today:
I broke down all of my brake masters, cleaned them of all 5606 traces, swapped the seals, and reassembled with DOT-4 fluid.
I did the same with the brake calipers.
I then did some more assembly work on the brake pedal assembly. I bolted the pedals in place and also the master cyl. I did not drill the lower mounting point to the brakes yet since I want to wait until the seats are in so I can optimize the geometry to fit me.