Skeleton put down.

SerialComms/SerialComms.pde

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+/* This sketch details serial communications over USB or XBee:
+q    - Query Status
+Q    - Query Verbose Status
+
+f    - Move Forwards 1 second
+F    - Move Forwards until stopped
+b    - Move Backwards 1 second
+B    - Move Backwards until stopped
+s    - Stop
+
+S    - Stop ALL (Including winch)
+
+u    - Winch up for 1 second
+U    - Winch up until home switch reached
+m    - Winch down for 1 second
+M    - Winch down for 5 seconds
+j    - Stop Winch
+
+i    - Toggle IR marker message ("--MARKER--");
+
+a    - Toggle move until IR hit then reverse
+R    - Reset
+*/
+
+#include <AFMotor.h>
+
+#define DEBUG 0
+
+#define IRSensor A0
+#define WinchHomeSwitch A1
+//Unused for now
+//#define WinchBarrelSwitch A2
+
+#define MarkerIRThreshhold 580
+
+#define SaneResenseTime 2000
+#define WinchDeadStopWait 75
+
+#define WheelMotorSpeed 255
+#define WinchMotorSpeed 255
+
+#define WinchLoweringDirection FORWARD
+#define WinchRaisingDirection BACKWARD
+
+#define WheelForwardDirection FORWARD
+#define WheelBackwardDirection BACKWARD
+
+
+/*
+#define MotionStart 0
+#define SenseWait 1
+#define WinchActionStart 2
+#define WinchActionWait 3
+*/
+
+//Globals
+AF_DCMotor wheelMotor(1, MOTOR12_8KHZ);
+AF_DCMotor winchMotor(2, MOTOR12_8KHZ);
+
+//State Globals
+boolean winchDown = false;
+
+boolean autoMove = false;
+
+int moveState = 0;
+int winchState = 0;
+
+boolean IRMarker = false;
+
+//Time globals
+unsigned long winchTime; //Used to wait for the winch to drop.
+unsigned long senseTimer; //Used to ride past the marker so we don't sense the same one twice.
+
+int readIR() {
+  return analogRead(IRSensor);
+}
+
+void winchDeadStop() {
+  winchMotor.run(winchDown ? WinchLoweringDirection : WinchRaisingDirection);
+  delay(WinchDeadStopWait);
+  winchMotor.run(RELEASE);
+}
+
+void setup() {
+  Serial.begin(9600);
+
+  //Set Pins.
+  pinMode(IRSensor, INPUT);
+  pinMode(WinchHomeSwitch, INPUT);
+
+  //Set Motors.
+  winchMotor.setSpeed(WinchMotorSpeed);
+  winchMotor.run(RELEASE);
+
+  wheelMotor.setSpeed(WheelMotorSpeed);
+  wheelMotor.run(RELEASE);
+
+
+}
+
+void loop() {
+  if( int bytes = Serial.available() ) {
+    char command = Serial.read();
+    switch(command) {
+     case 'Q':
+       Serial.println("Verbose state query: ");
+       break;
+       case 'q':
+       Serial.println("State query: ");
+
+       break;
+     case 'f':
+       Serial.println("Move forward, 1 second");
+
+       break;
+     case 'F':
+       Serial.println("Move forward until stopped");
+
+       break;
+     case 'b':
+       Serial.println("Move backward, 1 second");
+
+       break;
+     case 'B':
+       Serial.println("Move backward until stopped");
+
+       break;
+     case 's':
+       Serial.println("Stopping all wheel movement");
+
+
+       break;
+     case 'S':
+       Serial.println("Stopping all actions");
+
+
+       break;
+     case 'u':
+       Serial.println("Winch up, 1 second.");
+
+       break;
+     case 'U':
+       Serial.println("Winch up until home.");
+
+       break;
+     case 'm':
+       Serial.println("Winch down, 1 second");
+
+       break;
+     case 'M':
+       Serial.println("Winch down, 5 seconds");
+
+       break;
+     case 'j':
+       Serial.println("Stop winch");
+
+       break;
+     case 'i':
+       //IR marker readout
+
+       break;
+     case 'a':
+       Serial.println("Toggling auto move");
+
+       break;
+     case 'R':
+       Serial.println("Resetting");
+
+       break;
+    }
+
+    Serial.flush();
+  }
+
+  boolean atMarker = false;
+  int irReading = readIR();
+  //IR Status Pump
+  if(irReading >= MarkerIRThreshhold) {
+    atMarker = true;
+  }
+
+  //Wheel Status Pump
+  if(
+
+  //Winch Status Pump
+
+}

docs/SerialComms

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+q - Query Status
+Q - Query Verbose Status 
+
+f - Move Forwards 1 second 
+F - Move Forwards until stopped 
+b - Move Backwards 1 second 
+B - Move Backwards until stopped 
+s - Stop 
+S - Stop ALL (Including winch) 
+
+u - Winch up for 1 second 
+U - Winch up until home switch reached 
+m - Winch down for 1 second 
+M - Winch down for 5 seconds 
+j - Stop Winch 
+
+i - Toggle IR marker message 
+
+a - Toggle move until IR hit then reverse
+R - Reset