I built Bittle, went through the calibration process using the ruler. However, some gaits had a marked asymmetry, as if it was limping. Starting calibration again showed that some joints were in fact misaligned. I have identified why this is the case. There is a small but still significant amount of lash (looseness) in the gears, so when doing the fine calibration, if you are adjusting by small increments, it may appear that there is no movement. To overcome this, I would suggest doing a reverse movement first, or increment in the same direction. This way the movement is not being absorbed by the lash in the gears. So instead of trying offset 4, then 3, then 2 try something like 4, then -5, then 3, then -5, then 2. This has worked well so far.
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Yes, taking the average of larger offsets should improve the precision of calibration.