I had a similar problem, and swapped all the parts over (cranks, bottom Bracket, pedals), only to find that the 'clicking' was my aluminum Zefal frame-mounted pump, mounted on the seat tube, rubbing against one of the bottle cage bolts (no cage on the seat tube, only bolts). The bolt had worn a groove in the pump, and the frame flexes just enough when pedalling that the bolt was clicking in and out of the groove.