The only tools I needed for scraping in the past is a surface plate, prussian blue (about 5 bucks), a scraper from Enco (about 5-10 dollars), and a stone to prep the scraper and rub down the burrs. Also possibly some rags.
Then to scrape, he would have to clean everything, blue his plate (thin or thick coat depending on how much he wanted to check - usually a thicker layer of blue at first then thinner layers later) and rub the base to the plate. Use long strokes at first then keep going to shorter strokes with each iteration (stroke from different angles each time). Then stone down the burrs. Clean everything then repeat until you have about 10-20 spots/sq in. Once the base and column were done, it would give him a solid fitting that wouldn't flex as much under pressure.
As the milling machine he uses tilts left and right, he would only have to align the front to back. When he was done, he wouldn't have the flex from the shims. As it is now, he has a 2 to 4 ft lever arm (with a 50+ lbs overhang from the milling head) flexing a 2.25 inch (1/2 of the 4.5 inch column plate) arm on the column plate. Depending on the column plate, he will have some flex each time he has some force on the arm.
My suggestion was a way to try and improve his alignment from the 0.003" that he would like to improve upon.
Bob