Hi igrek,
I think the simplest solution would be to write a KFLOP C Program to watch the motion progress and generate your pulses. KFLOP User Programs basically execute every 180us so the pulses would have that resolution. This should be ~100X better than you could get from MS Windows.
The ch->Dest variable for the axis is the currently commanded Stepper position.
I have attached a Tangential Knife example that does something similar. It watches the motion and every time it detects a certain amount of motion then it calculates the direction and so forth. Your case would simply need to detect the motion then pulse.
HTH
Regards