Well I managed to get some time yesterday to sit down with the box of tricks and...she's a winner.

Created a 3.5" boot disk from the Apple site, unplugged the Disk ][ controller card, re-configured the slots (set slot 6 to be onboard disk controller) and it booted up no problems. Then powered down, plugged the Disk ][ controller into slot 7 and the boot disk happily now sees all three drives. Even inserted my 5.25" Apple /// boot disk in and it spotted it (I know, I'm sad but I just don't have any other 5.25" disks lying about).

Mucho big thanks to all involved