Hello, and welcome to the forum.
When choosing components I would try to avoid those using ferromagnetic materials. However, I would not have thought that standard SM resistors and capacitors would have been an issue. Do you really need to use a crystal? Can you make use of the internal reference within the MCU (assuming a MC9S08 MCU type)? If you need an accurate bus frequency, perhaps the use of a low frequency watch crystal would be better than a higher frequency crystal.
I think that you will ultimately need to experiment with the placement of any suspect components, to test their effect on the 3-axis measurement. I would certainly check the intended battery placement.
Another consideration might be the placement of PCB tracks in the vicinity of the sensor, especially for those carrying any significant current. I guess there should not be any of these tracks immediately below the sensor. For a PCB track that passes the sensor at a distance of 10mm, the flux density at the sensor position caused by the track current would be about 0.02uT per mA, using the formula B = u0*I /(2*pi*d). Compare this with the sensor sensitivity of 0.1uT per LSB.
Regards,
Mac