I appreciate the help so far :-)
It's a 300W ATX CPU and the 5V seems fine, the apollo 060 runs rock solid at 80MHz.
The A1200 has had timing fixes and caps replaced by Amigakit, had to do this for the ACA1231 to work.
I've checked the pass through connector it appears to be okay, can't see anything weird going on and the contacts on the A1200 look good, gave it a quick clean.
Not sure about cleaning the pass through connector though.
I've tried it with just the Voodoo card on it's own in various slots. I haven't even attempted to get the sound working. It does detect the SB128 and it shows in AHI but no sound.
No hiss/click on boot either, will have another look at the pass through :-/