robot_localization navsat_transform yaw offset and phidgets imu

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It's not so much that you need the offset; you just need an earth-referenced heading. The yaw_offset and magnetic_declination parameters are there to allow you to compensate for the fact that (a) most magnetometers read 0 at north, not east, and (b) they read 0 at magnetic north, not true north.

So you could just calculate that heading from course over ground and generate a sensor_msgs/Imu message that navsat_transform_node would listen to instead of your actual IMU message. Just make sure it conforms to standards: a heading of 0 means you are moving directly east, and turning left is positive rotation. I would imagine course over ground assumes 0 at north, so you can either manually adjust for that in your course-over-ground-heading-node, or you can set yaw_offset to pi/2.