So... I think I got it sorted. I left both hard drives plugged in (main as master, CF as slave). I then booted with a Workbench disk, followed the guide to put PFS3 on my drive (I was going to get all fancy with partitioning, but just left one big 4g partition cos I was getting a bit cranky at that point)
On reboot, I unplugged the good drive and left the CF card as master. Sure enough there was DH0 waiting for a format. Hit the format button and voila! a fresh new pfs3 format (quick of course). I am in the process of installing 3.1 onto the cf card, so in a few minutes or five I should be good to go.