For an encoder measurement, you need a counter and for pwm output, you need a digital line. In your case, that would mean a minimum two counters and one digital line. Have a look at the following webpage to find the right data acquisition device:
http://www.ni.com/dataacquisition/
You will need to decide on the form factor (PCI, USB etc.) and other things that will help you reach a decision. I would also recommend contacting your local NI office, to find a sales engineer to help you make that decision.
