Just downloaded your work and it looks fantastic, well done and I can't express enough my appreciation for your work. It's just fantastic, even just playing around with the LCD connections and the breadboard is great, I can see how easy things are going to be showing students in class how to wire up their circuits.
I have slightly modified the layout of the power and input / output pins (this is so you can use shorter wires due to most of the I/O pins being basically in the centre now) - I have attached a screenshot of how they have been re-arranged. Also, the screw connectors on the variable power supply are not used. They are a permanent fixture of the design with the left two connections being the 5V input from the USB port and the right two connections being the boosted variable output. these two connections then go to the four GND connections and the four VARIABLE connections which I think you were referring to above. Hopefully the screenshot clarifies this. The buttons are labelled B3, B2, B1 and B0 and then for the LED's in the buttons, they are labelled - L3, L2, L1 and L0.
Also I thought I should mention, the Arduino Uno is upside down in the image because it plugs in to the Education Board. however these pins aren't accessible at the Arduino, but down at the POWER AND INPUTS / OUTPUTS section.