If you would change to "continous pulses" you wouldn´t need a second counter per task, thats right. To count the generated pulses you would need a counter. So this does not improve your situation, still you would need two counter per motor. Best would be to use a counter-card (660x).
Maybe you could use an analog input, to count your generated pulses, but this will create a lot of overhead (you have to acquire your signal at a high rate and analyze de acquired signal to detect the number of pulses).
So from my point of view I don´t see a solution with your current hardware. You will need four counter for this application, so you either have to add a second multifunction board or use a counter-card.
Hope this helps!
André