To answer a few questions:
No bearings were lost when installing(rebuilding) the new ballnut on the ballscrew...I'm becoming an expert at rebuilding these now after so many teardowns.

The prelaod is set as per the IH instructions (.2turns) if I lossen it it will probably bind less, but that will just mask the problem. I have the Y axis working at the same preload with no binding. Gene wants me to try backing off the preload a bit but i would rather be certain the ballsrew is aligned perfectly b4 trying that.

wildcat, good suggestion on checking the ballsrew alignment i will do this next. I was trying to determine a good way to check the aligment previously.
The funny thing is I get binding on two far ends at time while the middle travel is fine. So that makes me think the ends may be out a bit. For that to be so the ballscrew may be slightly bend ( which seems to be the case when I turn the screw i notice a very slight wobble at free floating end. I though that this would not be an issue since the screw is quite flexible on the floating end.
What prelaod setting are you guys/gals using? Gene tells me you don't really need the full .2 turns? If your using less preload that .2 turns, any issues?

Also, the coolar on my ballnut seems to wiggle back and forth a bit on the two pins. Anyone see an issue with that in terms or backlash?