I will no longer be working on this project as such.
I'm really happy with how this ended up; It worked a treat for the core functions of what I needed it to do in terms of a platform I could prototype ideas on.
It still had a long way to go to refine features and also tidy cable management and take it to a level where it looked and functioned like I wanted.
I have recently bought one of the official Pi Touchscreens, along with a Raspberry Pi 3. I am aiming to turn this into the programming platform I've needed for so long :-)
As far as doing this I want to design an enclosure for my Arduino Mega with a the lcd shield attached. This case will feature a tiny breadboard and expose the analog and end digital pins on the Mega.
The combination of the breadboard and available pins will give me a great prototyping 'extension' to my touchscreen setup, and the inclusion of the LDC shield with buttons will allow plenty of options for communicating with the Pi via the serial connection. In future I may expand this to include either an EPS8266 module or a bluetooth module to provide further communication options.
Once I've given this more though I'll most likely start a new project.