Hi Slinger,
I took a cursory look at your project, but I'm no electronics expert, so take all my comments with a grain of salt.
Just looking at the circuitry, the PCB design looks very similar to the layout of the buttonbox, as shown here:
http://w1.132.telia.com/~u13205992/buttonbox/bbox2/pictures.htmNote: I said SIMILAR, I realize the actual compnents used are different and am NOT accusing you of copying their design. Mainly I wanted to point out for others that your design will probably have the same features (and drawbacks) as building a ButtonBox.
Other Comments - I notice your design uses Matrix Mode. I am familiar with this from keyboard hacking and usually (with keyboards), you are limited to the number of rows in the matrix (without ghosting/blocking). I.E. a 16x8 matrix keyboard has 16 available key assignments. Since you and ButtonBox both say there are no blocking problems in matrix mode, I assume you have a solution that avoids this.
Most users are more familiar with using direct mode encoders. There is no real problem with Matrix Mode, except, you have to convert things yourself (i.e. input 11 means I want to connect Row 2 and Column 3, etc.)
I realize you are still trying to get the prototype developed, but once this is done, could you post details on how to get 96 inputs with the unit.
Also, I think these would be much more successful if they were available pre-assembled, FWIW!!!
Anyway, thanks for posting the details and I look forward to more information as it becomes available.