Z-Axis Issues

So while I was building the Mendel, I had a number of issues with the Z-Axis. The first issue I had was that the threaded rod I got to drive the Z-Axis was not straight. I didn't realize this until I had it assembled. The Z-Axis kept binding when I tried to turn it by hand. After pulling it apart again I realized that the rods were not straight. I ordered some new higher grade stainless steel threaded rod from McMaster Carr. Once I got this cut and assembled it worked better.

However I feel that the entire design for the Z-Axis is a bit fiddly and I'm still having problems with it. It really depends on absolutely perfectly printed parts that are 100% flat. Mine aren't. There are a lot of parts to it and a build defect in any one of them can cause issues. Anytime either end of the axis mount is twisted the slightest bit, the nuts bind on the threaded rod and the Z-Axis becomes impossible to move. If you look in the picture below you will see the non-motor end of the Z-Axis. Notice the space between the bearing and the smooth rod for the Z-Axis. If I try to tighten this bearing up to close the gap it twists the axis and binds it. Still not quite sure how I'm going to overcome this.

If I am able to get the Mendel printing with a fair degree of accuracy. I may look into printing a set of Prusa Z-Axis mounts as they seem much simpler and potentially more reliable.