Losing steps will occur due to mechanical issue, electrical issue or both.
From what you describe, I would have a look at the cables inside the box with the drives of your 6040. There is no feedback between the motors and your controllers so the triping is caused by either cables being loose in sockets or generally bad cable installation.
Have you swapped all the cables with good shielded ones and made ground star point? Have a look at the couplers between the motors and the screws, under vibration they can come loose and slip.


By the way, that little controller looks cute from what I saw on youtube.