RICH,
Once again, thanks for the great info. Much of the concepts are familiar to me from research, and also my experiences with tweaking my 60 year old manual machines to work at their "best."
I love the idea of checking torque. Can you tell me the type of indicator you use? I only have torque wrenches for the motorcycles, which I use often and may be able to rig something up that can at least measure the differences in torque required - but likely not accurate measurements of the actual torque (any adapters will throw off proper calibrated measurement). But I think the torque differences would be the telling measurement while reassembling the axis to recognize the misalignment etc.
This is a brand new build, and the parts I had cut before this Z issue developed were plenty accurate enough for my needs. None of the parts we make for motorcycles are mission critical (you are not going to crash due to failure/tolerances of anything we make). But getting the machine to be as accurate as possible - and more importantly repeatable, is something I am more than willing to spend the energy on. It's time well spent.
You have made that job easier with your help and thorough explanations.
Attached is an example of a part cut on this machine. The satisfaction of cutting it, and then mounting it perfectly to the bike is amazing!
Thanks again!
Scott