Thanks...I am an office guy for a living but that engineering education has to pay off sometimes
I believe I spent about as much time measuring and building measuring jigs as I did cutting parts and assembling.
I have to watch that. So far I tried to stay away from setscrews (or grub screws) at least on the lead screw side of the coupling because I don't want to mess up the ends of my pretty C5 grade precision lead screws where I may have to take off the ballnut sometimes (remember the fixed bearing is on the other end). If really necessary I may use setscrews with brass tips like McMaster is selling.
I am quite satisfied with the distance parallelity, I got it to better than 2/1000", that is within the uncertainty of my dial gage jig. I measured using a 3" wide strip of plywood that I can rest against the sides of both rails with another square wood strip attached that is riding on top of the lower rail. The dial indicator is bolted to the plywood strip and measures against the bottom side of the upper rail (you can see this contraption in the picture on the table) and I can watch the indicator change while sliding along the rails.
I am not entirely happy with the twist. I hope it is good enough but the top rail ended about 10/1000" out of plane across the length. Not sure how I screwed that up but if I end up with tramming problems due to this twist I will have to go back and move the top rail.
That is actually how I got precision alignment: I built the gantry from bottom to top starting at the X-rails, measuring parallel and perpendicular alignment over and over with every new piece being attached and sanding or planing until it fits exactly. Basically one side of the gantry box every day. Since everything is glued and screwed together there is no room for error. Once the glue sets I can only start over. I made especially sure the rail mounting surfaces were already parallel, perpendicular to the table and straight.
The rails were then set in epoxy (actually J-B Weld because it does not easily drip or run) for leveling. The fine tuning of the parallel adjustment was done with moderate force by 4 or 5 clamps. Once the epoxy had cured, I drilled the bolt holes through the existing holes in the rails, countersunk and fastened the bolts.
I noticed building such a rigid structure comes at the price of serious accuracy requirements. A flexible machine is much more forgiving to assembly errors.