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You're running pulleys with 3mm id bearings on M3 threads? With washers for spacers? So many things wrong there. First, the bearing inner needs to be fixed to the shaft so the bearing outer can turn on the ball bearings, or you have hardened steel bearing on the soft, pointy screw threads. M3 threads are actually 2.89mm not 3mm diameter, If the bearings are a fraction tight then they will just chew up the threads and your pulleys won't run right. Second, the bearing outer needs to be free to turn so jamming a washer up against it defeats the point of having a bearing.
You need a shaft that's a tight fit in the bearing id, and spacers that only contact the lip of the inner race. Ok, so I can't find an easy solution there, at least not one that's available to buy. Best I can think of is some 3mm drill rod, held in place with epoxy, with a drop of ca glue to stop the pulleys wandering. I'm fortunate to have a lathe and a mill so I'll make some brass shafts and spacers.
Otherwise, great job, many thanks for all your hard work. I'm building mine atm, having a lot of fun as my bank balance diminishes.
Originally posted as a comment on your Youtube video 'HyperCube Evolution #4 - Y Axis Assembly': https://www.youtube.com/watch?v=lPyLJxsCRE4 - posted here to maybe help others.