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For the mag data, you'd have to either rotate the IMU so that the "new" X-axis (east) points forward, or just provide a static transform for that data. For the accelerometer and gyro, you can just negate the Y and Z axis values so that everything is ROS-conformant.
The EKF will transform the IMU data using the static transforms you provide before fusing the data. However, I think you'd be wise to just set the lever arms using the SBG calibration tool. I've worked with that exact sensor in the past in an underwater robotics application, and I went that route, rather than using static transforms.
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