Woohoo, I now have a fully functioning prototype stick built

Thanks to the hard work of dev and Toodles in the
Shoryuken pad-hacking thread, they set me in the right direction (unfortunately what they discovered didn't work exactly the same for me) and I've just had a quick match of Tekken 5 DR on my PS3 via a Logic3 PS2 to PS3 convertor.
The final wiring was as you'd expect for the controls but a little different for the ground wires.
1 ground wire daisy-chained to all of the controls apart from start and select. This then soldered on to a 4K7 Ohm resistor which in turn is soldered to Pin #3 of the section marked VR1 on the main PCB. Then another wire soldered on to the same resistor going in to pin 11 of the ribbon connector (the normal ground point for the controls).
For start, select and analog (if you need it), a ground wire coming from pin 10 on the ribbon connector daisy chained to the start, select and analog buttons.
Dave