Shiz AN-S are one of the best and heaviest knee mills ever built. Looks like you scored and have put a lot of elbow grease into the old girl.
I'm guessing you acquired it with the Emerson drives, and a breakout? Sounds as though someone had done or was doing a retrofit before you?
In order to receive help, your audience will need to know model and make of your interface or break-out board. Any pictures of it or electrical wiring diagram for it will help you and others to help you immensely.
It is also unclear if you are trying to use the old Shiz's pneumatic/ mechanical variable speed drive to adjust the spindle sheaves or using a vfd (although none in phot or mentioned.)
With servos, limit switches become more important for safety and prevent mechanical failures (crashes).
A common approach that I like, is to start with a single axis, e.g. 'X', mechanically disconnect the motor from the ballscrew, wire and test each component and function. MACH3 -> drive -> motor, Mach3/drive <- encoder, Mach 3 <- X=, X-, Xhome, After or while confirming outputs are functional, verify Mach 3 display axis/spindle direction are in agreement with direction, then magnitude or location. This will get you through all the necessities and familiarity of a single loop, rinse, repeat, rinse, repeat....
Save the spindle motor and speed for a later day.
Good lucks, congrats, and looks like you have a 'keeper.'