So after opening the case and put the printer on little blocks, today I've loosened the belts a bit and lowered the vref of the Y-driver from 1.1V to 0.9V and it looks like it's printing okay now. Will report if the print succeeds or fails
Edit: I've found a very good Reddit post on the subject. He has exactly the same as me (layer shift + thumb sound) and has a few videos where everything is quiet clear when it happens.
Edit 2: still some layer shifting happening. Better than before but still there. So still not usable on bigger prints.