I'd recommend taking your time, and walking through step by step, to see what is binding and why... seems obvious I know. Depending on how the ball-nut is mounted, it may be a simple matter of shimming the bottom edge of the mount to rotate that mount a bit, to provide clearance. Though, given that it only binds at the top, the top, the screw may not be parallel with the z axis; do you have a dial indicator, or a dial test indicator?
One thing you can try is to drop the head all the way to the bottom, then take a dial indicator (if you don't have one, Harbor Freight sells a servicable model for between $10 and $20 depending on the coupons you have), and measure the distance between the z-axis dovetail, and the ball screw (measure with the point in the "valley" of the screw). This should be as close as you can make it (definitely within 0.001"). If it's not, adjust the top/bottom brackets to get it there. If that is straight, check the distance from the face of the column, to the screw using the same method. You should be close there too.
If that all looks good, you can check the bearings by rotating the ball-screw 1/4 turn, then doing the same test. If you don't get the same results, then you have runout in the bearings. If it's real bad, then call the mfg and see about a replacement.
If all that seems straight, then I would check the alignment of the ball-nut mount. As I said above, if this is the issue, just shimming the bottom may be all you need.
