You were able to get it a whole lot better than you started off with. I think you need to just slowly modify the
shimming and you can do better. I will assume that the table is ground flat in the x and Y direction and you can check it easily if you have a straight edge ( just use a feeler gauge and see if it will go under at any point (stone the edge of a piece of .001" shim stock or see if you can detect any light under the straight edge ) say for 6" circle under the center of the collet.
You need some reference to work to so make sure the table is ok as a reference. Now do one direction at a time
If your out in one direction over 4" by .003", then shim 1/2 of it, test and repeat,etc...get one direction correct, for example the y direction reads the same as the indicator is rotated 180 degrees. Now do the x direction. When you have them as good as you can do, then put a piece of ground rod / drill blank into the collet and check the spindle. A machinist square against the rod will quickly show you how square the spindle is to the table FOR THAT COLLET only.
You can have runout on the spindle or the collet and over say 3 or 4" you may have 1 or 2 thou.
You need to work from a known reference and then check everthing one.... step ..... at a time.
BTW, when shimming place a small piece near the bolt or edge only since a different size shim may be required at each of the four bolts in the column base.
Take your time, be patience, Have A Happy New Year,
RICH