[ace123]

One thing that I would suggest is to change the part of user_routines_fast.c that says /*DO NOT CHANGE*/

No real code changes, but it is just a small thing to run something when it begins and ends... This is legal, and the "do not change" comment is referring to changing the order or deleting the loop.

void User_Autonomous_Code(void)
{
  /* Initialize all PWMs and Relays when entering Autonomous mode, or else it
     will be stuck with the last values mapped from the joysticks.  Remember, 
     even when Disabled it is reading inputs from the Operator Interface. 
  */
  pwm01=pwm02=pwm03=pwm04=0;
  pwm05=pwm06=pwm07=pwm08=0;
  pwm09=pwm10=pwm11=pwm12=0;
  pwm13=pwm14=pwm15=pwm16=0;

  printf("Autonomous mode has begun!!!\r");
  // Code executes here when autonomous begins...;
  // Use this to reset all autonomous state variables (if any)

  do {
    if (statusflag.NEW_SPI_DATA)      /* 26.2ms loop area */
    {
      Getdata(&rxdata);   /* DO NOT DELETE, or you will be stuck here forever! */
      if (!autonomous_mode) { // Autonomous stopped.

        printf("Autonomous mode has ended!!!\r");
        // Code executes here when autonomous mode ends...
        // Use this to stop camera, stop all motors.

      } else {

        // Normal autonomous code

      }
      Generate_Pwms(pwm13,pwm14,pwm15,pwm16);
      Putdata(&txdata);   /* DO NOT DELETE, or you will get no PWM outputs! */
    }
  } while (autonomous_mode);   /* DO NOT CHANGE! */
}

Alternatives that require setting variables while in autonomous mode, etc. are a lot messier than a few if statements in the loop.