For added Z height, you could probably make some spacer blocks to lift the whole X/Y gantry above the table, similar to a mill column spacer. That could give you increased Z clearance, but wouldn't increase Z travel (so you could end up being unable to reach all the way to the table). But there would be ways to compensate for that, like installing a sacrificial pallet. Ideally, you would use some solid steel bars that are match ground parallel, but even steel bars that are fly cut on a mill, or the CNC itself, should be adequate. You'd probably need to fly-cut the table flat if you were using just milled parts. Getting a couple of steel bars ground parallel shouldn't be too expensive though, if there's a shop near you that does surface grinding. I presume you could probably run a small fly cutter in it. Size would be limited as the shank is 1/2", but you should be able to use a ~2" diameter fly cutter with a low depth of cut. That would be a fairly big project though to get set up properly and something you wouldn't want to be swapping in and out all the time. Having just trammed the column of my mill, it's a bit of a pain. Every bolt that you tighten moves things. If you did get the 3-axis, you could probably increase its accuracy by getting some parts of it surface ground. Looking at the photos, the construction looks to be mostly formed plates that are welded together. I would imagine that the relevant surfaces are machined after they are welded together, but they are unlikely to be ground. So, if you were having trouble with or trying to get more precision out of it, you could have the surfaces that the linear bearings mount on ground flat and parallel. But, you're talking probably a difference in a few tenths over the length of travel.