A couple of more thoughts:
-Was any maintenance performed, or any changes/modifications made to the bike shortly before the noise started? There could be a clue there.
-On the bottom bracket thought: Do you have the correct spacing via washers and wavy washers? If the crank has too much slop in bottom bracket width it can move side to side when pedaling and you would only hear it when pedaling.
(With all these annoying noises, if only someone could invent a bicycle where no two parts come into direct contact with each other.)