What are the lengths of the Z-axis tubes? I probably missed it somewhere but I was thinking 12".
Thanks!
That should be fine. (Mine is only 11" 
)
The center assembly is about 6" thick, and you need another 2" for the top of the Z assembly, so that would leave you 4" of Z movement. Seeing as router bits are only about 2" long, that’s more than enough unless you’re doing something very unusual.
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This dimension is (IMO) the easiest place to pick up rigidity. Since the bits aren’t that long, making the Z short will help with learning. Don’t forget the spoil board and the feet have a minimum height.
The calculator will help you go from a Z height to pipe length.
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Extra length hanging out the top is generally harmless and can save you having to cut the lead screw, and then you can reach down farther if you install a drop table.
I would just set the z travel to the lead screw length as far as the z axis assembly goes, and the short legs keep the working height low so you have good stiffness.
Lowrider or mpcnc?
Oh oops I was thinking mpcnc, but same should apply to LR, right?
Oh, I missed that. Yeah, on the low rider, it gets less rigid the higher you go. On the mpcnc, it gets less rigid the lower you go. So disregard my earlier advice.