That Eagle schematic is quite out of date. This was for I was for the single board with IO Expander and 4 encoders that I was building. I made a prototype with veroboard, but gave up because I had horrible mechanical problems. It was very difficult to drill the holes for the encoders and align them to the cutout for the display. Then I discovered that I'd placed the 40 way connector in the wrong place & gave up (after a lot of screaming...)
I've learnt from my mistakes & I'm concentrating on my second build. It uses a 5 inch HDMI display. I've designed a 'breakout' board that plugs to the Raspberry PI with wired connections to the encoders. The board is on it's way from China. I'll share details with the group when it's all tested.