G59,
Try these settings
CN04 Speed Loop Gain, set it to 00032
CN05 Speed Loop Integration Time, set it to 00030
CN1A Position Loop Gain, set it to 00040
Kevin is correct the CN2 connector does not matter when running this with the software it controls all the functions using software.
If you have no AC power near those encoder wires it should not matter. If you have an AC wire near the encoder cable it can make it not work correctly.
Russ