Ive postponed/ abandoned the project some time ago, but I do not recall having that same problem with a different batch of steppers and while using a lighter needle. But I also switched from arduino to an esp32 and used interrupts to drive the microsteps. I also made some changes to the switecx12 library acceleration values.
Which of those cured it, I do not know or remember, but if it helps, I posted the code here:
From what you say, I doubt you have problems with stepper motor, and I suspect your best bet is using a microstepper controller.