I go through this at least once a season on a customers bike. It's tough because as hard as it is for you to determine the sound, it's almost as hard for us. The steps you've mentioned are the same ones I would take. Pedals, un-lubed seat tubes, a SLIGHTLY loose headset, loose QR's and a range of other things have been causes. One time I helped a customer who who was having this issue and we went trough the ENTIRE bike. Nothing. Then one day, we pulled off his bottle cage and the was the smallest crack around one of the bosses. Just to check, some JB Weld was applied, and the noise was gone. The frame was warrantied, and everyone was happy.

Sometimes things like this can be frustrating for everyone involved. Just try to be nice about it.