Tramming the head would not solve the problem stated in this thread...The "Machinist" approach is simple. Put a finger indicator (or dial test indicator) in the spindle and bring it down to the table surface and Zero it. Rotate the spindle by hand and sweep it from side to side and front to back making sure it is Zero in all the quadrants every 90 deg. Loosen the bolts that hold the head keeping one slightly tighter than finger tight to piviot on, and tap the head from side to side using a DEAD BLOW HAMMER to tram it in. If it is off from front to back then your mounting plate may need to be either shimmed or milled flat. As you tighten the mounting bolts the head might move so tram and tighten at the same time until every bolt is tight. I would also use tread locker (not the permanent type) on the bolts so they do not come loose from vibration. You will typically need to do this from time to time in the event the tool runs into anything forcing the head out of sq.
Hope this makes sence to you.
the problem experinced here comes from the colum not being square to the table. It comes into play or becomes noticable when you use drill bits of different length (i.e. center bit then drill bit) The only way to fix this problem is to tram the spindle in square to the table. With column misalignment you actually get Y or X axis travel at the tool bit as the Z axis is traversed. The Op. stated that his holes were off in the X direction so this would indicate the column needing to be tilted one way or the other.