Acceleration setting - how much margin?

Do a "worst case scenario" configuration, in your case as i understood the moving table mill/router, you have to actually load the max weight that your machine might see during use, plus the forces used during cutting, so you have to load the table and push or pull on the opposite direction while tuning. You can use a small hanging scale for weight measuring ( i use a small one for cnc machines that do no cutting, it can measure up to 35 kg, for machines that have to cut i just test while cutting a a higher feed rate ), it is handy for having some idea of what are the forces exerted on the machine.
After tuning to worst case scenario, you can move back 10% and be fairly certain that you will not have any issues during normal use.
You can do all the possible calculations in the world, and it will all come back to that, namely practice, not theory. To many moving parts and forces and gravity and inertia and............so a bit of trial and error is all it takes.
Regards,
Tom
B.TH.W.
on bigger machines i climb on the gantry, i push against them or pull them as hard as i can to have a sense of how much force it takes to stall them or make them loose steps. Sometimes it gets .........painful !!!

fswizard will calculate tool forces. Put in your worst-case material and the biggest tool and see what the numbers are.