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So adding a static transform between the IMU and the base_link seems to have solved the first issue.

<node pkg="tf" type="static_transform_publisher" name="static_transform_publisher3" args="0 0 0.3 0 0 0 1 base_link imu_msg 100"/>

Now getting:

[FATAL] [1478348520.099726403]: F1105 12:22:00.000000 17582 imu_tracker.cc:66] Check failed: (orientation_ * gravity_vector_).z() > 0. (nan vs. 0)

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