So - after an ongoing argument and a massive amount messing around, plus a small spot of engineering and swearing - I finally managed to get the camera to connect to my computer!
So the heat sync got cutup to fit [warning graphic content!]
And this is the unit laid out - it all fits and is a pleasure to use. The one issue I've had is that occasionally during loading of some games the HDMI screen decides it has to turn off and won't turn back on so I'll have to wire up another button to trigger that occasionally.
Edit: So I wired the screen power button to the gamepad "power" button which has worked really well, and I sincerely hope there's not another button I need as I'm kinda all out! I also tracked down the lines to power the little LED light behind the home button, but couldn't access the PS2 lights anymore as I glued the memory card over them. So being lazy wired it to the analogue light on the controller - and oddly enough you wouldn't believe how happy that little glowing light makes me. I wonder if I need glowing sticks now...