Alhtough this answer should be awarded to Pete, because he has spotted it first.
The accelerometer has a sensitivity of 5%, which corresponds to 100[mV/g]. what you are measuring is 0.1[m/s^2], which is about 0.01g. So the actual signal you should be receiving from the piezoelectric accelerometer is about 1[mV], which is quite low.
Now, if you see the ...
The "three plate" method has been used as the basis for precision manufacturing/inspection. This
is a decent summary, it's pretty ingenious and only requires dye and abrasives.
This will teach you everything you need to know and then some, "Foundations of Mechanical Accuracy".
You must first calibrate your three devices to give the same result against each other for at least two different input values. A one-point calibration only assures that they have no baseline constant offset relative to each other for the given input. Two points assures that the devices are linear in the same way over the calibration range. Three points and ...
You are using a piezo electric accelerometer. There are always always always offsets and low frequency noise on a piezoelectric accel. Depending on the charge amp, anything below about 3 hz is meaningless. Just high pass filter the signal to get rid of it. If you need to read below 3 hz then you shouldn't use a piezoelectric. Use mems or piezo resistive in ...
there is a whole genre of "square block" videos on YouTube by various machinists. The standard tool seems to be the lathe.
But really, you are asking how to set up a machine to be perpendicular.
apropos, video for your edumatainment