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Isabella and I are working on a solution but I'm constrained to spending a few short periods per day at the keyboard so it's taking a while to "pull it all together", however, the route we are taking is to increase the number of connections by using shift registers. This has no limit on the number of in and out pins it can support but it gets slower as you increase the number of connections so it may not be suitable for your application.
If you're looking for a clean out of the box solution I might say try looking at getting a data acquisition card (DAQ) National Instruments is a good starting place they also have a straight forward graphical programming suite called LabVIEW where you can control your IO and make a fair GUI. (but ewww.... LabVIEW! makes me shiver!). This will be expensive, however there are 3rd party companies that make DAQ cards for LabVIEW and Matlab.
A nice cheap way would be to use an FPGA... grab an el-chepo development kit with plenty of IO (see Digalent - they have a good range of kits as well as breakout boards) and the sky is the limit as to what you could do! the easiest way, off the top of my head would be to set up two 100bit buses (in and out) have a simple state machine sample the bus and pump it into a serial core byte at a time (13 bytes) and pump them into a PC. You would also concurrently be concatenating the Rx data bytes, and writing them to the output bus. You might need to work on a simple protocol so things don't get messed up, but that's the jist of it anyway. Of course your max sample and update rate would be dependent on the serial baud... @115200 this would be about 1ms or 1kHz.
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