Sounds like the problem got solved, but I'll add my bit: we had a similar mysterious noise. I pulled out both bottom brackets, re-greased the threads & eccentric to eliminate any metal-metal creaking, and the creaking disappeared for a while. But it returned. We tried diagnosing with my stoker pedalling (no noise) and with me pedaling (creaking present), which was why we thought it was somewhere in the captain's cockpit. Wrong. It was loose chainring bolts on the stoker's timing crank. The noise had disappeared when I did the bottom bracket work because I tightened up the timing chain just enough to eliminate any play in the rear timing chainring. I guess the noise didn't show up when we tried to diagnose it with only my stoker pedalling, because there was no pressure on the timing chain.
Moral of the story: when you are going through long checklist of things that cause mysterious creaking noises, check that the chainring bolts are tight!