After a few weeks of use, I decided to check the tension on my belts and make sure everything is square on my machine. Also, after a few weeks of attempting to level my bed in vane, I finally capitulated and skimmed the wasteboard with 0.75" flycutter. My primary use for my x-carve is building tools and other more precise objects, so I need as much accuracy as I can muster. One of the things I’ve noticed is the Z-axis is very slightly out of square. This was most evident after I skimmed my board with the 0.75" bit, which, given it’s large contact area, allowed me to pick up a very slight misalignment as each of the passes had a very discreet, but still discernable, lip. It would seem the gantry (as with nearly all structures in some sense) goes out of square when a load is applied. Naturally, because the tool piece is offset from the gantry by a good 4-5" this is probably inevitable. I will say the rigidity of the new gantry is impressive, to say the least; however, I have a feeling the slop is stacked tolerances across the gantry, v-wheels, and lead screw. Althought it may sound like nitpicking, this kind of deflection on a deep cut could result in problems. My question is, are the more accuracy minded x-carve operators adjusting for this by adding a slight correction Z axis to bring the tool head square under a load?
Also, after much searching on the forum, I’m left with a generalized question regarding an accepted method for calibrating the machine across all the axis. It seems there are several different methods, but I couldn’t find a consensus. If anyone has a particular thread or method they prefer, primarily focused on the X and Y axis, I’d love to hear it. I would assume a simple circle would tell you a lot.
Are you using the stock Z axis?
I am, yes. I have seen a few upgrades being done around the board. I wondered if the money was best spend on a new Z axis, or if it would be better spent on just designing a totally different (more rigid) machine. First, I needed a functional machine before I could build a new one. I’m trying to get a gauge on what the X-carve’s capabilities are, and what my expectations should be.
The V Wheels on the z axis are a large source of flex and the belt drive can be a source of lost steps. You can square up the z axis by placing shims between it and where it mounts on the x carriage. This however, won’t remove the flex. A linear bearing z is much more rigid. I’m not sue what accuracy others are getting with it. perhaps @PhilJohnson, @Clyde or @MarcCohen once he gets his running might comment on this. I will once I get mine back in one piece. 
The X-carve is capable of, what I consider to be, very good accuracy. Its expected you can get within .003" or better on softer material such as wood or plastic. I don’t know what people are getting with metals. IMHO if you are doing wood and you need better than this I would look at a professional model. If you are doing metal a cnc mill would be best.
I inserted a shim between the aluminum rail the Z-axis rids on and the gantry ‘box’ that it attaches to. Worked for me.