I agree with Mark that it isn't legal to place a limit switch inline with a motor.
We've typically chosen two options from the following list:
- Limit Switch with software control
- Potentiometer or Encoder with PID control and soft limits
- Current sensor
- Mechanism robust enough that it doesn't matter
Another option is to use the limit switch inputs on the jaguars, which will operate faster then your software and won't get commented out accidentally.