So, I just thought I'd put this thing to bed for future reference.
After about 200 miles on my new brake parts, the clicking noise has returned.
In summary, the only non-OEM parts are the discs, they're EBC, surely they are to blame?
I've read that this phenomenum exists on factory new bikes, I'm going to ignore it. The brakes work very well. At least I have a spare set of EBC pads which, if I ever need to fit them, may click to their heart's content. That's provided that I don't have to replace the discs for OEM ones in the meantime. Yikes!