Edit: attached the configs for parallel port and Mesa board.
Here is the updated video with the issue sorted out, had to do a lot of editing of hal and ini, so i had missed an error there that was causing one direction to not work properly.
Now it works perfectly smooth on both directions.
The motor has two protrusions that is why the DVM shows double the frequency, Linuxcnc shows correctly 2000mm/m and that is 2000RPM on the motor as it is scaled to 1mm per revolution.
With some tuning the Ferror is very small, so all in all, very nice results so far.
Added the arduino nano as it has 8 analogue inputs, will connect the IS pins (current sense on the drives, two on each) to those analogue inputs, and the enables to arduino outputs. Also will connect one output from Mesa 6i25 to arduino digital input, it is set as charge pump so arduino should enable the drives only when the charge pump signal is present and disable them in case any of the IS output goes over the threshold set, that will have to be adjusted after the motors are mounted and tested to find the current limits. This also makes possible wiring of the other outputs from the arduino to the other Mesa 6i25 port since there are another 4 encoders there and use that to show the actual load of each axis in each direction.
All this seems unnecessary as the drives will not work if both PWM inputs are set high, so that is a nice security feature, some other drives i have will run the motor at full speed in such a case. This is just more functionality and better overall security.
3 days on this, not very smart, but since i had the stuff thought I'd give it a go.