Houston, we have a problem. How can I ensure that the X axis rails are parallel to each other? Just so we're all reading from the same page, let me refresh your memory of what this thing looks like.

Starting in the lower LH corner we have what I am going to call the west side, because that's the way the machine is actually oriented. The X axis rails are the longer set of rails running east-west, with the Y axis being the shorter set of rails that run north-south. Keep in mind that the gantry is fixed and the bed moves east and west along the X axis, The spindle moves north and south along the Y axis rails.
The magenta colored objects that are 50mm from each corner of the frame are the standoffs that hold the frame about 6mm off the base. Those standoffs are there, because there's a lump in the base. As near as I can tell, using the edge of a carpenter's square for a straight edge, the east, north, and west edges of the base are flat. The lump is about 0.008"-0.010" thick, and is centered about 100mm from the south edge of the base, and about 1/2 of the length of the machine from the west end. Except on the south side, I know those standoffs are in areas that are flat. The 6mm gap should allow the machine frame to bridge the lump, so the top of the frame should be flat to the east, west, and north sides of the base. So hopefully, this will allow me to ignore the lump.
So here M'Lords, is my clever plan, at least for the X axis alignment:
1 - I'm going to level the east, west, and north edges of the base. I've got a precision level, it's not a great precision level, but it's got to be better than a carpenters level. I've got some leveling feet on order that should make that job a little easer.
2 - After the base is level, I'm going to level the frame to the base. I'll level it both north-south, and east-west, that'll ensure there's no twist in the frame. I'm hoping it will already BE level, but... Hope for the best and plan for the worst. If the frame isn't level, fixing that will involve shimming it level. Since everything else is somehow related to those side frames, getting them true to the world will make life easier for Future Don. I got some 5/16" thick float glass that is used to hone wood working tools "scary sharp", this and my 1-2-3 blocks should allow me to bridge over the bed and check that the frames are level - both north-south and east-west. JBWorxStudio uses the float glass to tram in the spindle of his CNC router, it should work for this too.
3 - Next will be checking that the rails are level, this will tell me if the vertical centerline of the rails are parallel to the top of the frame. I'm REALLY hoping that the rails will be level to the frame, since the mounting bolts for the rails use the 2 side slots in the 2040 side frame extrusions. There may be a little wiggle room there, but not a whole lot of it.
4 - Next on the hit parade will be checking the bed, The bed should be level, it does ride on the X axis rails after all. But, those linear bearing mounting brackets were fabricated early in this project, before I knew how critical attention to detail REALLY was. If they aren't level, I'll probably have to slot the mounting holes for now, and make new brackets when I get this thing operational. I also need to be sure slots of the bed are perpendicular to the side frames. a 6" square fill do for now.
Once I've got the bed level, I can start the process of getting the Y axis rails aligned.