@Iggy_D
Yes, the manual is essential when fitting a Catweasel to a 1200 mobo (or a Zorro 4 bus) because it doesn't correspond to the usual convention regarding the 'red' lead/Pin 1.
I burned out my Catweasel because of this and I know I'm not the first! Luckily, PowerComputing fixed it for free.
I don't think the IDE idea is a good one. There's nothing in the manual to suggest this approach. Anyway, I doubt that the connectors will match up (?)
The latest multidisk.device driver eliminates the earlier dependency to use clock port 0. See if that resolves your problems.
Cheers,
JaX