Yea like Kip said, in mach3 you have the options to setup and make the adjustments you need to. Once your machine is up and running, you then go in and fine tune everything as you need to.

I'm also designing a Z axis at the moment, I will be looking to get around 100mm travel on that axis, I think the thing to look at would be the purpose of the machine, what you would be likely to cut with it and then base things around that.

My machine is going to be for very light work really, predominately cutting through 3mm ply, over a distance of about 4'x2'. So I want a machine that will be accurate, strong and at the same time have quite a good cutting speed so it keeps everything viable over having the parts cut on something like a laser machine.

As such my z axis doesn’t really need allot of travel but dose need to be well made and ideally using supported linear rails.

Hope this helps you in some way.