The first thing i would do, would be to run a DFT on the sensor signal and see if there is actually a high and low frequency component of your accelerometer signals.
With a DFT you should be able to determine an optimum cutoff frequency of your lowpass/bandpass filter.
If you have a constant component on the Z axis, there is a chance that you haven't filtered out gravity. Note that if there is a significant pitch or roll this constant can be seen on your X and Y axes as well
Generally pose estimation with an accelerometer is not a good idea as you need to integrate the acceleration signals twice to get a pose. If the signal is noisy you are going to be in trouble already after a couple of seconds if the noise is not 100% evenly distributed between + and -.
If we assume that there is no noise coming from your gears, even the conversion accuracy of the Accelerometer might start to mess up your pose after a couple of minutes.
I would definately use a second sensor, eg a compass/encoder in combination with your mathematical model and combine all your sensor data in a kalmann filter(Sensor fusion).
You might also be able to derive a black box model of your noise by assuming that it is correlated with your motors RPM. (Box-jenkins/Arma/Arima).