Anilam CrusaderM to Linuxcnc Mesa 7i77 + 5i25

What is the resolution of your scales?

scale = 0.0005"

head (reader) = 0.0005"

.0012 is within 3 counts so probably about as good as you are going to be able to
do with your limited scale resolution. A small amount of I term in your PID loops
may be able to keep the no load static error within 1 count

Would rotary encoders on the motor be a possible solution ?