Is the home position off in all three axis or just Z?
Assuming Z only, from your post... Is the screw which activates the Z axis endstop loose, i.e. the screw is not being held in a fixed position because the spring is not compressed? If the screw becomes loose the extruder will be too low and hit the glass. I think I had to fit a 40mm screw rather than the 30mm one in the instructions to get the adjustment and a bit of tension in the spring to prevent it moving. You shouldn't have to recalibrate the machine each print once it's been set correctly.
Does the Z endstop microswitch work correctly? The Z axis should drive downwards till the switch state changes then back up till it changes back causing it to stop. Even though microswitches are pretty simple devices, the places where it changes from open to closed to open should be pretty constant. Maybe the switch is faulty? You could try replacing it or swapping with one of the other axies. If the fault changes axis, the switch definitely needs replaced.
My two cents
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Soadyheid