MesaCT 2.1.8: Scale vs Encoder Scale

Dear all, I am new to Linuxcnc and trying to setup a bench test before connecting motors to my machine. I got Stepperonline A6 series 400W that allow analog control. I setup velocity mode on them and I setup a mesa 7i97T to control them with analog signal and get a feedback from the servo drive. I am sure I nailed all the wiring properly, but when I setup the MesaCT 2.1.8 to generate the configuration file I have doubts on what to put into the tool when it comes to selecting the axis Scale and then the encoder scale. My A6 drive have 17bit encoders that translate into 131072 pulse/rev. But I also see in the drive parameter that it is set by default 2500 lines ( that in quadrature should be 10000pulse/rev). my max velocity in the drive is set to 3000rpm.

My confusion is now to understand what parameters to input in the mesact config. for now I just want to test a motor (x axis) without any connection. Can someone expert chime in on the value to input in Max Velocity, Max acceleration, axis Scale, and encoder scale, to make this run and proceed to next step PID calibration? 
What I need is a clear explanation on what is SCALE vs Encoder Scale input field. I seem to be confused when I read the manual of the mesact. They seem to be the same thing. I understand that the scale should be calculated based on gear ration between encoder and motor etc etc. In my case the encoder is the motor encoder and the SCALE of the axis is for now not connected to anything. The plan is later to place this motor on a 1604 leadscrew (4 mm pitch).

Thanks in advance and apologies for this novice question, but could not find anywhere a clear explanation.

The maximum attainable velocity for an axis is √(maxaccleration*axistravel)

3000rpm*4mm/rev = 12000mm/minute, which is more than enough.

Your axis scale is 4mm/rev, I believe.

The encoder scale with a 4mm pitch screw and 10000 counts per turn would be
2500 (counts per mm)

Not sure on MesaCT what the other scale refers to but possibly analog output scaling

LinuxCNCs maximum velocity should typically be about 80% of the drives maximum velocity
to allow control headroom. So with a 3000 RPM maximum drive speed, 160 mm/sec would
be a good maximum velocity (3000 RPM=50 RPS so 200 mm/s woudl be the velocity at 3000 RPM).
A good guess at maximum acceleration is 5X the maximum velocity
so 800 mm/s^2 (this means an axis will get to full speed in 1/5 of a second)

There are a number of tuning tutorials on the forum, assuming the drives are setup for velocity mode,
the most critical tuning parameter is FF1. If you set the analog scale to 200 (because at 10V the linear velocity
would be 200 mm/s) , FF1 will be 1.00