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Thanks for the nicely formatted question! I'm not positive this will do anything, but before I start looking at bag files, I do see that your navsat_transform_node instance is listening to the wrong EKF output. navsat_transform_node will work with a two-level EKF setup, but doesn't require it, so this line in your navsat_transform_node configuration:

<remap from="odometry/filtered" to="$(arg local_odom)"/>

should be

<remap from="odometry/filtered" to="$(arg global_odom)"/>

The circular dependency between navsat_transform_node and the EKF is intentional. Again, I'm not sure that's your issue, but we should fix it before continuing.