Gotta agree with 31 ROC, having 3 pedals and rowing through the gears is a big part of the fun.
A lot of great information here. I still think the under the floor set-up is still your best option. A lot less fabrication and easier access.
Cut out the drivers side floor pan, install the pedals assembly, then install a new floor pan that fits around the pedals and that has access doors for the master cylinders. All this can be done in a fairly accessible area and it will be hidden once your done.
Here is a shot of my floor pan area for comparison. Old photo, that has been scanned, but thought it might be usefull: