MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
I'm willing to bet you it's the spiral couplers, I chased my tail with them until I used an oldham coupler of my own design, and then designed a magnetic coupler which worked great, I never got around to publishing those designs, but there is a similar one here: https://www.thingiverse.com/thing:804873
The idea is no side forces get transferred to the Z-rod, and the Z rod will need bearings at both ends of course.
Some people have had luck with this:https://www.banggood.com/5mm-x-8mm-Aluminum-Flexible-Spider-Shaft-Coupling-OD25mm-x-L30mm-CNC-Stepper-Motor-Coupler-Connector-p-995515.html?cur_warehouse=CN
Or go with the Z-belts, I made it that way for this Z-banding problem.