a few months ago I had a similar mysterious click that did not go with the pedal stroke. it was the chain, I had an outside link plate coming loose and it would make noise every now and again going thru the cassette. the smaller the gear (numerically) the more pronounced it was, in the big sprockets there was less stress on it and made slightly less noise. by the time everything was said and done I ended up busting a chain and damaging the derailluer hanger.