Did you setup the centre line using a depth gague in the milling chuck. Checking for offset close to the rotary chuck and then at the tailstock and the adjusting height of tailstock to suit? Just a thought.
I like your mods.
I have an X2 as well and had all sorts of issues with it out of the box in terms of rigidity and too much play on the axis.
I haven't upgraded the drive yet as the gear drive has been ok for me so far though very noisy.
I converted the cheap threaded rod axis to ball rod...
I also use a piece of paper. Slide it around as you lower the tool onto it. When it just grips the paper that's it. Generally I don't worry about adjusting for the thickness of the paper unless close toloreance needed.