Hello guys,
Thanks for the answers!
The short belts are tight and pulleys on the motor shafts are tight aswell. I have put a mark on those pulleys/shafts aswell so i can see it when they have moved.
The X and Y axis are square to each other. I can move the head by hand when powered off without too much resistance. I did lubcriate the axis a bit with some sewing machine oil, but that didn't make any difference.
I will try Didier's solution to re-route the wires from the end stops to prevent an cross-talk.