sounds like you are looking for a data logger to me. You could probably find plenty of designs using google. There may be some out there that are mostly software, with a PC recording in real time through the serial bus.
What kind of encoders are you using? Hopefully not optical, they can fail a lot. Do the encoders output serial or analog besides the PWM you seem to be using? If analog, you could modify a PC O-scope design. If PWM you could use a uC to change the PWM to serial data, and send to PC.
Hope that gives you some ideas.