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Hi Jonas,
There are four things that come to my mind.
1, Hangprinter designs with Nema17 motors are useing quite hugh reduction gears to gain power and resolution (steps/mm). How big are your pulleys and what reduction gear you use?
2, If you rely just on the internal gearbox froget 1:16 version of 28BYJ-48 and 12V rated motors. The only version that can be used with bipolar hack in printers is 1:64 5V version. And even than, you realy need to get them runing because output power = speed * torque. That explains why you can run 1000mm/min, but not 100mm/min. You simply do not have enough power at low speeds.
3, The torque of 1:64 version is good enough to move slowly light weight carriage with linear bearings on precision rods by slightly tensioned timing belts. You are on the other hand moving the whole printer on outputshafts of three motors, that do not have even bearings inside. You are bending the shafts to the side, possibly damaging the internal gearbox as the teeth are jamming. Is there any way how to catch the radial load comming from pulleys with some bearing and use the 28BYJ-48 only to turn the pulleys?
4, Possibly there is some problem in the firmware that is causing this strange behaviour or you are simply lacking steps/mm so what you expereince is printer jumping from one step to another. But microstepping will help you only to some extent.

I would definetly recomend to add 6 bearings (2 form each side of every pulley+use some screws as pulley shaft and join them with motor shafts by some flexible coupling. Also use geared extruder instead of direct drive. Feel free to remix mine. Again for the same reasons. Shaft of the motor is not under side stress and also the motor is turnig four times more compared to direct drive so it is four times more powerfull when extruding.

Hope that will help
Rergards
Martin