my 6040 experience (yeah, and problems) so far

[EddyCurrent]

Answer to some of your points.

Not saying this is your problem but I had ball trouble too, see here for how I solved it; http://www.mycncuk.com/threads/6565-...6350#post56350
If you run the ball nut up and down by hand you will see if the problem lies with that, it could be the end bearings or the screw is bent, http://www.mycncuk.com/threads/6565-...6172#post56172 or it's mounted out of line. I also had problems with the BK type bearings blocks but not sure if yours uses that type. http://www.mycncuk.com/threads/6565-...6128#post56128

This is the right grease for linear bearings as well, some people use oil for both instead of grease.
http://www.toolstation.com/shop/Auto...0/sd180/p89691

On the Ports and Pins / Motor Outputs screen, if you want to reverse the directions of any of the axes, toggle the "Dir Low Active" checkbox for that motor.

Good thread here about spindles cooling etc.
http://www.mycncuk.com/threads/5814-...nd-Advice-More