With both rudder cables connected, I was able to check full travel of the rudder and rudder pedals. It appears that I don't need to provide clearance for full pedal travel to provide sufficient rudder travel. This reduction in pedal travel means less issue with the pedals and brake assemblies impinging on the retract torque tubes. The reduction isn't a large amount but it does help.

Having checked master cylinder travel on a couple of other completed airplanes, I don't think I'll need full travel on these master cylinders. Following that theory, means that I can shorten the master cylinder pistons slightly. I shortened the master cylinder pistons by 5/16". This reduces the overall relaxed length of the master cylinder by that same amount, providing more room for fitment.