Ronan,
Yaw axis is always the biggest challenge. It works for the handheld gimbal systems but is more limited on a Multirotor.
You have to re-calibrate the gyros much more frequently for the Yaw axis IMU as they drift a lot.
If you have a heavy camera, the Yaw motor torque becomes a critical factor.
Also you have to first hang your BGC/camera system at 90 degrees to carefully balance the yaw axis..... critical!
For Multirotors you have to stick with the "Heading" mode for now versus "Follow Mode".
So get "Heading" mode working first before tackling bigger challenges.
I am going to assume that you pinned down the number of motor poles based on motor model number data and/or counted the motor coils then added 2 as best guess could lead you astray.
The weakness of the low cost IMUs used on BGCs becomes most apparent with the Yaw axis due to the gyro drift.
There is not enough sensor input information available from these to enable the BGC to maintain a "follow" mode with accuracy for a longer period of time.
In other words, the AlexMOS is not there yet relative to the Radian and other very expensive complete solutions.
It was working fine before though... That's what has me puzzled...
Heck now it doesn't even know it's front from back...