Hi Tom
This starts alarm bells with me
"as the PO has cut and shut the whole set-up while attaching it to a huge frame of blue painted angle iron, I assume in an effort to get rid of any vibration"
A sturdy angle iron frame that has any distortion from welding will distort the cast iron frame on the mill and cause misalignment problem.
A quick check loosen the hold down bolts and check if there is clearance under the feet of the mill with a feeler guages.
Fabricate shims to that thickness and fit to the offending bolt do not tighten just yet.
Lock the all Gibs with the table in approximately the middle of the travel
Fit a Dial Test Indicator on an arm from the spindle and check the reading on the dial with the plunger on the outside end of the table and write it down.
Repeat on the other corners
Tighten the holding down bolts and recheck the four DTI readings
If all four are the same as the original readings you have it right first time.
If not them you will have to add shim where the DTI shows that the base has distorted.
You can Add a washer under the feet to make it a bit easier to shim true
Or use Short jacking screws and adjusting nuts Look at an example in my Photo Album.
Eric