Originally Posted by
skrubol
If you can fit a rail on top without getting in the way of your screw, that is a fairly common way to mount a second rail, it's often better than 2 rails on the front, but harder to align.
You definitely don't want more room between the bed and the gantry than you need. You're right that longer Z extension is bad (not only does it add more opportunity for flex in the Z, it will want to twist the gantry more.) Stiffness is the square of thickness (all else equal,) so .25" steel isn't super stiff compared to something with a frame, but it's mostly a lack of stiffness in the Z axis, where it's probably least likely to show. Also if your vise is bridging most of the space between the rails that will stiffen things up as well. Aluminum extrusions can be quite stiff, but most of the machines made out of the thinner stuff are pretty wimpy.
I'll take a look at your spindle thread as well.
Machine certainly performs better than it looks!