Hi, thanks a lot for your feedback, it always helps !
I wanted to make a hole to fit a m3 nut but I forgot to do it. Though, if you just put a m3 screw there, it will prevent the pulley from going off and the screw will be blocked axially by the X-axis rod. The 20T pulleys do not rub on mine but it is quite tight indeed so with different print settings or a different printer it may cause problems. Same goes for the X-gantry (I guess you are taking about the whole X-axis carrier) because mine lined perfectly with the frame. I'd like to find a way to give a bit more of flexibility on these parts bit it's not easy.