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Just as update, extremely sorry for the lateness in reply.
So i was misinterpreting how ekf was fusing the wheel odometry and the IMU. Despite having orientation correct from IMU the X,Y position odometry from the wheels was very off due to a differential drive odometry calculation node having some wrong parameters.
Specifically the wheel width between the two wheels was too small and I had to increase by almost 2 times to get accurate turning (I did this by just guess and check) . Now the ekf output is matching the actual robot movement.
Also I have ekf also fusing position estimate from an indoor GPS which is now giving a more accurate position estimate.
I am however getting a different set of issues now regarding orientation, the y direction movement is flipped in the global frame... Should I create new post for that issue?