If i had to attempt something this size my plan of attack would be weld the main frame, make the pads on your uprights a good thickness, after welding spot face the pads so you have a flat surface for taking shim sizes, on your top rails have some good thick pads to mate with the ones on the frame, send your two top rails away for machining of top suface and pads plus the sides for ballscrew alignment, align the top rails and measure for shims.
just my opinion
Hope it helps.
Regards
Mike