If you are seeing a series of step-like features when you face with multiple passes, they can be attributed to an out of tram condition. As Tom said, loose gibs can cause this problem. If the z axis gib is loose, the head will be sagging slightly and the front side of the facing tool will be cutting deeper than the back side. If you can lock the z axis ways, this should reduce that sagging condition.
On a manual mill, this isn't a problem as you would lock the axes that weren't moving but on a CNC machine, generally, all three axes are free to move. (A CNC facing routine would typically make a pass, lift to a safe height move to the start of the next pass, and lower to cutting depth for the next pass.)
A loose z axis gib can also cause the head to rotate slightly due to play in the ways and the cutting forces. You would see this in the pattern left by the cutting tool. The circular arcs will appear different when facing in opposite directions.
If you are tightening your gibs, be careful not to over-tighten. Over-tightening will increase backlash and wear on the ways and in extreme cases, can lead to lost steps in your stepper motor on the affected axis.
Sweeping the table with an indicator is not an indication of out of tram condition. It is measuring the parallelness of the table surface with the x and y axes. I noticed that your mill has a havel spec for fully supported travel and maximum travel. Ideally, you will be operating in the region of full table support. Loose ways and an unsupported table can result in table lift. On my Tormach 770, this happens at 10" to the left of home position in the x direction.
In a final analysis, .001" over 9" is not a huge problem. You are just over .0001"/" which is as good as many 1-2-3 blocks and precision squares. If it were my machine, I would work with it a while before I attempted any adjustments.