If positive PID output and positive encoder counts do not correspond to positive axis movement on your particular machine, then you just need to set the "Direction Reversed" option on the Machine Configuration -> Motor Parameters table.
Yes, the axes will run away if you enable them while uncoupled from the encoders.
The reason you are not able to close the E-stop contactor with stall detection enabled is probably because your X and Z encoders are both showing differential errors:
Code: Select all
(1) 09-04-2021 13:31:27 406 Emergency stop detected
(1) 09-04-2021 13:31:56 412 X axis(1) encoder differential error
(1) 09-04-2021 13:31:56 412 Z axis(3) encoder differential error
(1) 09-04-2021 13:32:06 412 X axis(1) encoder differential error
(1) 09-04-2021 13:32:06 412 Z axis(3) encoder differential error
(1) 09-04-2021 13:32:08 406 Emergency stop detected
See:
and also:
http://www.cncsnw.com/EncoderTest.htm