I dpnt think figure it out is the right phrase. You are talking about big, heavy peices of machinery.
I think your best approach is to start low and gradually work up to what you consider is a safe speed for the chunk of metal that is flying about.
I dont know what speeds you are expecting, so cannot really comment, but I would keep the acceleration low to start with, since it is this that will cause the problems, not necessarily the speed.
How long is the maximum travel.
Using the Mach3 stepper motor configuration, I would set the acceleration so the table reaches maximum speed half through the maximum travel (as per the graph on the syystem). Keep increasing the speed until you reach what you consider the maximum safe speed, then gradually ramp up the acceleration to get you to maximum speed more quickly