You've got some nice hardware there Lynn, but the z in the current configuration is not very useful except for engraving of thin materials. You ideally need another higher rail, to spread the distance apart for your z axis, and a clearance of around 3 inches really is at the very least desirable. I would consider mandatory for any use. 4 inches below the lowest point is better, but ensure you allow enough height for tooling, and accessing the cutters with materials under the spindle.
Can you raise the x axis higher in the gantry, and maybe fit a supported round rail along the top, with an upside-down "L" plate to then mount your z axis on?
The forces from any decent machining or routing will cause massive amounts of flex and twist otherwise. You should be able to push reasonably hard on the axis and not have any detectable movement. As under load this will be very apparent. Also, do you have any bracing under your table as the rails are in a bit from the end, and you'll likely find machining side to side the ends will not end up machined the same depth as the middle section. Although this of course depends entirely on what you plan to machine.
cheers, Ian
It's rumoured that everytime someone buys a TB6560 based board, an engineer cries!