Two other areas to check but according to your description #2 might be the one. I had this issue with my new wheelset.

1) Check the cassette.
Is it loose? A loose cassette will generate clicks.
Is one cog loose? A cog not properly inserted on the hub (possible with Campy) will make a clicking noise when in use as it is allowed to make a back and forth small revolution on the hub.

2) Are you using tubes with threadless stems. My Michelin tube stem made noise on rough roads as they were banging on the rim wall. Pinch the stem between two fingers and shake them, if they make a rattle noise use a tubes with threaded stems or use some tape.