I have Nema 23 motors that are driven by a G540. 

The setting for the first one I figured by experimenting and getting the machine to move precisely 40" when it said it moved 40". 

But what is the best procedure for the rest?  How do I know what maximum velocity or acceleration should be?

Counts
Per Unit: 6350

Velocity
Units/Minute: 200

Acceleration
Units/Sec ²: 60.33

I'm sure there is some more scientific way to do this... but this has always worked for us.  Using steppers. 
Set the acceleration to 10% of your Velocity. 
Set the velocity as high as you can without stalling the steppers; (trial and error) then back off that number by about 1/3 so you know you'll always be in the range your motors can handle. 

I'll give it a go. 

Thank you!