3/4" master cylinder?

Duster,
You make some very good points that people rarely think about. Such as how the m/c connects to the pedal. I have made several brake pedals over the years for different applications. With brakes applied, a line drawn through the pedal pivot-m/c connection point should be at 90* with m/c shaft for max transfer of the pedal force. A small diam m/c will have more pedal travel, all else being equal, then a large diam m/c. So getting this angle correct is a bit more complex; may need a new pedal or a piece welded onto it that allows a new pivot hole to be drilled for the 90* angle.

I think you may have nailed it... just went out and looked (drove it to work today) and i am hitting 90* at only about 1" of pedal travel.. Looks like the box will come out pretty easily, will modify it this weekend (move the pivot forward and down a small bit) and it should fix it. It does feel just like my cobra before i did the fix, so... This would also explain why chasing parts didn't fix anything.