Okay, so here is version two (actually, more like version four). I've lowered the rudder pedals by three inches. This required that I make some "forks" to go over the master cylinders in order to be able to connect them to the brake pedals in their original locations. I also moved the master cylinders to the center of each pedal, and added another "ear" to each brake pedal to distribute the load more evenly.
Now I can comfortably activate each brake pedal, even with the rudder pedal fully deflected. I may need to extend those lugs in the center to give more rudder travel, but we'll see how that works out when I hook up the rudder itself. And of course now that the work is done, I realize that since there won't be any brake pedals on the passenger side, I probably should have left those rudder pedals at their original height, in order to be more comfortable for the passenger.
Total Time: 20.5 hrs.