So you had the pads re faced???
Ive never heard of that happening before outside of race teams...
I bet you one of the pads is out, cause what you have described is what happens when you get old pads on new discs...
or new pads on old warped and very well used discs...
It causes a vibration and sometimes a clicking noise...
Id be checking the pads are true...
Apart from that the only other thing that can make a click or clunk noise is a loose bolt/fitting/pad...
Check the pads, re-bleed the system make sure there i no air in the lines and tripple check all bolts etc...
Also visually inspect the discs and see where the wear marks are on th disc, that will be a good indication of if my hunch is right...