I've replaced (or tested should I say, because in fact I'm about to replace) the motors for different ones. The current model I use are 400 steps JK42HM40-0406 and I was unable to get a smooth and silent operation out of them even though I use the Trinamic's TMC2130 for driving. After come testing I was left with this result table :

And I've decided to go with the 17HS4401. I don't know why my 400 steps ones caused so many problems, the only culprit is the much higher coil resistance which could make current sensing difficult for the drivers. But I'm not sure. I'd love to hear someone's insight on this. And here is the picture for today, the current state of electronics. I plan to design a dedicated board and hide it inside one of those supports you can see on the both sides of the plotter.