[Mark McLeod]

PWM_in1 through 6 are from the first Vex receiver port
PWM_in7 through 12 are from the second Vex receiver port.

So...

// Driver Control - Rx1 preferably
  pwm03 = PWM_in1;  // Depends on what mode you select on the transmitter
pwm04 = PWM_in2;

//Arm Control - Rx2 preferably
pwm01 = PWM_in7; //- Arm raise/lower (on CH 1 of 2nd transmitter)
pwm02 = PWM_in9; //- Arm extend/retract (on CH 3 of 2nd transmitter)
pwm05 = PWM_in11; //- Servo to lock arm (on CH 5 of 2nd transmitter)

In ifi_aliases.h you'll see them:

/*
 *-------------------------------------------------------------------------------
 *---------- Aliases for R/C PWM IN connectors -------------------------------
 *-------------------------------------------------------------------------------
 *  Below are aliases for the PWM inputs received from the radio-control receiver.
 */
#define PWM_in1         rxdata.oi_analog01
#define PWM_in2         rxdata.oi_analog02
#define PWM_in3         rxdata.oi_analog03
#define PWM_in4         rxdata.oi_analog04
#define PWM_in5         rxdata.oi_analog05
#define PWM_in6         rxdata.oi_analog06

#define PWM_in7         rxdata.oi_analog07
#define PWM_in8         rxdata.oi_analog08
#define PWM_in9         rxdata.oi_analog09
#define PWM_in10        rxdata.oi_analog10
#define PWM_in11        rxdata.oi_analog11
#define PWM_in12        rxdata.oi_analog12