Hello Kevin,
I mounted my base on height adjustable feet which are themselves part of raising blocks so that I could get the machine X Y axis handles above the lip of a swarf tray I made for it. The underside of my base is ground but I really have no idea if those surfaces are parallel with the Y axis guides; machine alignment for bolting down was to get the table level in both axes.
If you build your machine onto the workbench in a similar way, supported at the 4 corners, I think you will avoid the need to do anything else and save quite a lot of effort and expense into the bargain
Over the years I've made some useful improvements to the design, in particular to the key acting on the column for head raising and incorporating a home made thrust bearing between the column and collar which contains that key. It halves the effort in winding the head up and down..
I would be very happy to share these and others with you if you are interested. While you have it stripped down might be a good time to build them in.
Email me wood [underscore] y [at] btinternet [dot] com no spaces and all in lower case.
Kind regards Brian