I may be able to help on some of these.... although not from direct experience. I just have seen others mention similar issues so I'll pass the general answers on.
1) The X2 machines have a lot of play in hole placement, so you may have to slightly tweak the holes on the kit to fit your machine. Generally, you shouldn't be applying force to your ballscrews to make them line up.
2) This is a known issue with some conversion kits. There are modifications you can make to the kit to allow you to get to the adjustment screws but I don't have a link handy... you can probably find it with some searching.
Noise/Binding has so many possible causes I can't help much there.
Q: How many tools does it take before a simple task becomes a project?
A: Just one. I'm the Tool that turns a simple task in to a project.