The ATYPE 45 is A+B quadrature output square wave and will work with a drive that has the same type of input.  alternatively ATYPE 43 outputs short pulses and a direction signal.

You set the UNITS to 16 x the normal value to allow for the divider in the MC508 pulse generator.  So for revs, it will be UNITS = 16 * counts_per_turn.

Then with SPEED = 1000 / 60 ' revs per second, the pulse edge rate will be 16.66667 Hz.  That is the correct frequency to drive the motor at 1000 RPM.