Before I completely tear this thing apart again here's a couple shots of what it looks like with the new rails installed.

I installed the mocked-up lead-nut assembly just as a sanity check - it fits so I guess I'm still sane.
Installing the X axis rails on the side frames is causing some issues.

That change, while it made the alignment of the machine
MUCH easier also threw a monkey wrench into some of the other stuff. There is no longer 1/4" between the bottom of the bed and the bearing blocks, it's more like 3-ish mm. I've got some 1/4"x1-1/2" aluminum angle that I will modify to make the bed/bearing mounting brackets. I'll lose another 3mm of Z work height, bringing the max working Z height down to about 60mm, but that will be fixed after I get this thing running again. It can make itself new extended Z height side plates. The X axis lead-nut mounting block will need to change. The current plan is to add 3mm to the dimensions of the existing mount, and print that. Then I install that lead-nut, measure how thick of a shim I need between the lead-nut and the bottom of the bed, print the shim, and install it - Eazzee-Peasee.