So after completing the project, we have since made two minor changes.
(1) The Raspberry Pi we used has been replaced with a Raspberry Pi Zero (much smaller than the standard Pi), and the speakers have been replaced by a fitted 'Speaker pHat' that sits on top of the Pi Zero. This has saved lots of room. The strange white cable is a USB connector that allows the Pi to access the school wifi - although anyone about to start a similar project might want to use the recently released Raspberry Pi Zero W (with built in Wifi).
(2) The analogue clock face now has the same background 3D printed shapes as the other faces.