JSBSim is using geocentric coordinates to compute the J2 gravity model. The computations are made in the file src/models/FGInertial.cpp

You can get the acceleration magnitude from accelerations/gravity-ft_sec2. I would not use the a-pilot-[xyz]-ft_sec2 properties since they are computed in the body frame and are therefore affected by Coriolis and centrifugal accelerations. I suppose that you want to integrate the accelerations in the inertial frame ?

No errors have been reported so far about the gravity model. However if you might be more specific about your findings that might help to solve your issue and fix the bugs if any. Please describe the result you obtain from JSBSim, how you obtained them as well as the result you are expecting.

Also for clarity, please avoid TLAs (Three Letters Acronyms) such as INS and EKF as this will make your statements clearer to everyone.

Thanks.