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Besides the coordinate frame problems @tfoote mentioned, your approach is flawed.

You publish the 90 deg mounting as /base_link -> imu_frame, then get that in your IMU node, apply the IMU transform and republish the same. From the outside, i.e. another tf user, this looks to be two different transforms (with/without) IMU orientation applied that contradict each other as both are giving a transformation between the same frames.

You could either include the 90 degree mount in the imu node and apply that only ever sending out the full transformation over tf, or split this up in two transforms. It seems to me that base_link -> imu should never change as it's mounted fixed. Using two transforms also means, you'll never have to apply the transformation, tf will do that.

hector_slam has an example of how such a setup might look like. Check the base_stabilized vs. the base_link.