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The problem sounds like maybe one of your stepper drivers is overheating and going into protection mode – they stop momentarily to allow the heat to dissipate. This is a common problem on a lot of 3D printers, usually alleviated by adding a small fan somewhere near the drivers.
So try that, just a little 30mm 5v or 12v fan blowing air across the stepper drivers. See if it makes a difference at all.