I check out the datasheet of L3GD20 (gyro) and LIS3DSH (acc). With respect to the position of Pin 1, they have different XYZ orientations.
Is there any reason why you think they should be aligned?
I needed to implement a kalmar filter with the gyro, accelerometer, and magnometer....and unless I am mistaken, wouldn't I need to know which axis is aligned with which and adjust accordingly?
My apologies for the delay in response. Depending on how you're using the kalman filter, you may or may not need to adjust for sensor displacement. If, however, it becomes necessary, there are algorithms that you can use in your code, or even modified kalman filters that will adjust for the displacement.