Well I've made some progress...
I inserted a SID chip (6581) taken from an old C64 that would only boot to a red screen. Unfortunately, no matter how I set the jumpers on the extender card, the C-One would refuse to boot and I would get a "drone" from the audio. Removing the chip and resetting the jumpers allowed me to boot as normal.
I added my 1.6GB ClassicWB hard file to the CF Card and had my Minimig core boot from that. Playing the WHDload games made me notice that my sound now worked perfectly! However, I still have the issue with the joystick not working correctly. I've replaced the root extender.rbf file from the minimig ZIP package (my CF card did have an older one) as you suggested, but it makes no difference.
So, I have Minimig sound, my SID chip doesn't work (might be a dead chip which explains why the C64 only booted to a red screen) and my joystick detection is still buggered.
Anyway, I'm glad to see my WHDLoad games off my Hard File working well.
Edit: Actually, I've just noticed I left 2 jumpers off the Extender Card - the ones you're only supoosed to remove if the sound is naff with the SID fitted.