Bryan,
Since I don't have one of these units and know absolutely nothing about them, this is more of a question that a suggestion. Is there no way that you could put some kind of heat reflecting insulation between your headers and the master cylinder? I used a chrome tape with high reflection quality on a couple of things in another car that were having heat problems as they were very close to the header tube and that solved that problem for the rest of the time that I had that vehicle.
As I stated, just asking as I don't have any idea of just how close or anything your set up is to the headers.
Ron