Looking at your log, it appears that you are not logging the IMU at the fast rate. My first suggestion is to change our LOG_BITMASK to one that includes fast IMU. Based on the data you provided, the frequency of the vibration that I could see was approximately 660 RPM. What is your head speed? What is the distance from the rotor shaft to the blade grip bolt? I can use this data to look at the blade lead-lag frequency. Trying to rule out causes, how tight are your blade grips? You want them tight enough to give some resistance but not overly tight that the blade is hard to move in the grip. A big concern that I would have with this type of configuration is structural based vibrations due to two rotating systems. If it was this type of vibration, it would be really bad at one rotor speed and then subside as you get above it, if you can get above it without a structural failure.
Neat project!