I suggest you back up a bit so we can all get on the same page.
To be clear, you are talking about the head travel being perpendicular to the table in both the x and y direction (the proper term here is "normal.")
This is a multi step process, and it is easy to waste your time.
These are the steps in order:
1) Make the head travel parallel to the column, you MUST do this first or all other adjustments are meaningless.
You mount the indicator to the column, and measure along a test bar in the spindle (use your method of choice, Rollie Dad is fine). You move the head, not the spindle. You can correct the x-axis by rotating the head, you correct the y-axis (this is called "nod") by shimming or scraping between the head and the column.
2) Make the column perpendicular to the table in the x and y direction.
You measure by mounting the indicator of the table and measuring along a test bar. Again, you move the head and not the spindle Minor adjustment to the x-axis can be done by shimming between the base and the stand. Correcting the y-axis requires shimming or scraping between the column and the base.
3) tram the head/quill. Here you get the best balance between head movement and spindle travel. If the 2 preceding steps where completed, then the head will be square to the table, and you will only see any mis-alignment between the spindle and the head. This mis-alignment should be pretty minimal, and you can safely rotated the head to compensate most of the time. If it is way out, then you will have decisions to make (live with it, scrape into shape, or replace).
This corrects minor errors from the other adjustments. Mainly it is used for getting the quill perpendicular in the x-axis after you rotated or crashed the head.
Image the column leaning over at an angle, but you have the head trammed to the table. When you lower the head, it moves diagonally down. Now think about what happens when you try to bore with a head that moves diagonally downward. It is really important for so many reasons that the head move parallel to the column and normal to the table. If this is done, then a cheap import that only cuts to a thou suddenly reliably cuts to under 5/10's.
Shimming between the machine and the stand is required for pretty much all bench style mills, you would be amazed how much even a flimsy stand will twist the base casting on a mill. Shimming between the base and the column will result in loss of rigidity, increased vibration, and other odd problems. Once the correct shim is figured out for the y-axis, the column should be bedded with the shim using a bedding compound like the way a gunsmith beds a rifle action, except you should use a release agent on both sides. Ideally it should be scrapped, but bedding is fine. Shimming between the head and the column will create the same problems as between the base and the column, with the added issue of what to do with the shim when you rotate the head. Scraping is the only real solution, because scraping will let you get it true even when the head is rotated.
Under no circumstance should you use set screws between the column and base or the head and the column where they will bear the force of the adjustment. You can use them to put the column into plum, bed the column, then back off the screws. I have seen people use set screws between the head and the column adaptor to get the head square to the table. This will just cause nothing but grief down the road because of the divots left by the set screws. Using set screws in little brackets to give micro-adjust to the head for tramming is an excellent mod, and will make your life easier.
