Your electronics box looks very well built, good job.
The little screw nuts on these machines I dont know if your backlash will hold up. With end bearings with no movement it is very possible to get this setup very tight. But the little flap with the set screw will more than likely ware quick.
Finishing your brass gibs will help as you have seen with the Z axis. So this will take more pressure off the screw/nut and may help it last longer. As you have seen these little nuts are not much, it would be possible to turn them into a backlash nut if you had more brass to make the parts to add to them ( using spring washers & screws to hold the second nut to take the place of that little flap).
You might even consider getting some of the derin anti backlash nuts that have the slit end and a spring assembly to take out backlash. The forces on this mill are very low so this kinda nut could work good. You would only need to make mounts for them. They also take less force away, unlike the style the X1 uses so it might even gain IPM. Not that you need it faster but it might help it be smoother , plus hold tight clearances longer.
As small as the screws are on this machine it would not cost much to add multy start screws with better accuracy & friction that can run these derin anty backlash nuts. With the mill run under CNC it would not be hard to make mounts for this setup. All though clearance for nuts under the table & sadle are very thin on a X1, so carefull measurements would need to be taken before so you would know if they fit.
Anyway your mill looks great, would love to see a video of it running. Its not to often you see someone put a lot of time into a X1. I am converting one now, but with a lot of mods. It has leanier rails & ball screws with a lot of axis extentions built in. I am stuck on it for now because of budget but i hope to get back on it soon.
BTW your spindle drive looks very interesting. I am guessing its a belt drive and you have done away with the box that held the electronics & gears. Looks like a nice job.
Jess
GOD Bless, and prayers for all.