Hey Shawn,
A simple low-pass filter can be constructed with a resistor and a capacitor. They are also called RC filters; R=resistor, C=capacitor. This combination gives you a cut-off frequency so your low frequency signals - like with limit switches - can pass while the higher frequency signals - like the motor drive voltages - are suppressed.
Using this
online calculator as reference, connect the wire coming from the limit switch to the resistor and the parallel port input to the junction of the other side of the resistor and the capacitor. The other end of the cap is then grounded. The values for a 500Hz low-pass are: resistor = 3K, cap = 0.1uF
Note that you want the RC filter as close to the parallel port as possible so it filters out the noise picked up by the wire coming from the limit switch. If you connect it in the control box right before the parallel cable to your PC, you should be good.
JR