Additionally you have to be careful with the fixture of the road. Also here you can create worst case 0.3mm misalignment (or compensate

ball bearings : Please check my assembly suggestion for the Y-axis ball bearing. Some additional washer ad a distance part really helps. I ruined my first bearing also and was wondering of Y-axis wobbling and missalignment...
A4988 drivers : The X-axis worked fine for me. Same for the Y-axis until I killed my bearings on the other side. Took me days to find you where the extra enormous forces would come from. Please check also your X-bearings. Maybe same problem.
X axis endstop : Agree. Thex changed the end-stops and now everything is 3mm to far away. Have problems with x,y, and Z and helped myself by some modifications.
firmware : Same issues (all of them). Really crap and the bad thing there is no source code to fix it. This is really pain in the ass.