So, I think I'm nearing a final design for my readout: I've decided to mount the LEDs and the LED Display directly onto the PCB. The PCB has to be slightly bigger, but once I realised I can mount things behind the LED Display, its' actually not such a big difference. It's still slightly bigger (and therefore more expensive) but the savings on connectors and cables pretty much evens it out. The PCB will have the function of the LEDs printed next to them. The major up-side is that the main board will just be able to be plugged directly into a USB socket and it will work. Giving me options for a phased delivery approach if there are problems in the final assembly.
Other major changes include putting all of the resistors on the board (As a result of having LEDs there) and adding an aux power connection for the servo. And I've found a USB/TTL adapter, and designed in the connection for that too, it just plugs straight into the board, so I don't have to worry too much about mounting it
I've mocked up the final layout on a paper print-out with the pins sticking into some polystyrene, showing both sides to confirm that the mirroring has worked as planned. Next step is a final breadboard prototype based solely on the PCB schematic, (hard-wiring the LED Display means I HAVE to get the pins right, one benefit of using a ribbon cable was that I could work out which way up it went when It was delivered) and I can finally order the PCB. The only one change (there's always one more) I intend to make, is to connect a few spare IO ports from the processor to pads for future proofing.