Motor1 does not have PWM, ArduinoUNO + Motor Shield

The problem I am having specifically is that motor 1 is sending out only an ON/OFF signal, with no variable speed control. I have done a little bit of research on this, and I have pretty much narrowed it down to the library for AFMotor. I am completely new to Arduino and programming in general (I have literally never touched either of them), but that is why I started my project. I want to learn some programming. Being my first project, it is pretty extensive lol. I am building a omni directional robot using mecanum wheels as the drivetrain, and controlled with a Playstation 3 controller. The robot also has a manipulator arm and a claw, which are two wire DC motors, but I have motor controllers for them to convert them to three wires, so I can use them as a servo. Though these don’t necessarily have to be speed controlled, I would at least like one of them to be.

As of right now, the setup is the Arduino UNO plus a USB host shield with a dongle and a motor shield on top of that. For each motor, I have two LED’s attached, in reverse direction of each other. One green (forward), one red (backwards). This way I don’t have to have a big power supply for testing purposes. Later I will modify the output motor speeds in the programming. Right now they are set relatively low, under 50%. That being said, motor 1 is at full power or off. I have already burnt up two LED’s just from testing, so I took them out completely.

So far my programming seems to be working correctly. I have it to where the left joystick controls the forward oriented movement, basically forward/backwards/strafe left/strafe right and the right joystick spins the robot. The LED’s do what they should but motor 1 does not change brightness. It stays at full power. It DOES change direction, so red comes on when its backwards and green for forward. Just no speed control.

Now the library I have read through and have found that it says that motor 1 will not have PWM, and all I need to do is jump pins 10 and 11, or 9 and 11 and just uncomment one of the lines in the library. But I do not know how to do this. I have tried opening it up in word and notepad and doing it that way, but that doesn’t seem to be the correct way to do it, and either way it did not work. So, what am I missing here? or how do I actually go about doing this?

Sorry for the long post, but I wanted you to have the most information possible before making the post.
I will post up the code if you like, but I know the code I have is not the problem. It is also not 100% complete, and it is very long.

Also here is a link for the library I was talking about, AFMotor.h
it says in there about the M1 not having PWM.
I have copy and pasted from the site to make it easier to see.

// Adafruit Motor shield library
// copyright Adafruit Industries LLC, 2009
// this code is public domain, enjoy!
* Usage Notes:
* For PIC32, all features work properly with the following two exceptions:
* 1) Because the PIC32 only has 5 PWM outputs, and the AFMotor shield needs 6
* to completely operate (four for motor outputs and two for RC servos), the
* M1 motor output will not have PWM ability when used with a PIC32 board.
* However, there is a very simple workaround. If you need to drive a stepper
* or DC motor with PWM on motor output M1, you can use the PWM output on pin
* 9 or pin 10 (normally use for RC servo outputs on Arduino, not needed for
* RC servo outputs on PIC32) to drive the PWM input for M1 by simply putting
* a jumber from pin 9 to pin 11 or pin 10 to pin 11. Then uncomment one of the
* two #defines below to activate the PWM on either pin 9 or pin 10. You will
* then have a fully functional microstepping for 2 stepper motors, or four
* DC motor outputs with PWM.
* 2) There is a conflict between RC Servo outputs on pins 9 and pins 10 and
* the operation of DC motors and stepper motors as of 9/2012. This issue
* will get fixed in future MPIDE releases, but at the present time it means
* that the Motor Party example will NOT work properly. Any time you attach
* an RC servo to pins 9 or pins 10, ALL PWM outputs on the whole board will
* stop working. Thus no steppers or DC motors.
// <BPS> 09/15/2012 Modified for use with chipKIT boards
#ifndef _AFMotor_h_
#define _AFMotor_h_
#include <inttypes.h>
#if defined(__AVR__)
#include <avr/io.h>
//#define MOTORDEBUG 1
#define MICROSTEPS 16 // 8 or 16
#define MOTOR12_64KHZ _BV(CS20) // no prescale
#define MOTOR12_8KHZ _BV(CS21) // divide by 8
#define MOTOR12_2KHZ _BV(CS21) | _BV(CS20) // divide by 32
#define MOTOR12_1KHZ _BV(CS22) // divide by 64
#define MOTOR34_64KHZ _BV(CS00) // no prescale
#define MOTOR34_8KHZ _BV(CS01) // divide by 8
#define MOTOR34_1KHZ _BV(CS01) | _BV(CS00) // divide by 64
#define DC_MOTOR_PWM_RATE MOTOR34_8KHZ // PWM rate for DC motors
#define STEPPER1_PWM_RATE MOTOR12_64KHZ // PWM rate for stepper 1
#define STEPPER2_PWM_RATE MOTOR34_64KHZ // PWM rate for stepper 2
#elif defined(__PIC32MX__)
//#define MOTORDEBUG 1
// Uncomment the one of following lines if you have put a jumper from
// either pin 9 to pin 11 or pin 10 to pin 11 on your Motor Shield.
// Either will enable PWM for M1
//#define PIC32_USE_PIN9_FOR_M1_PWM
//#define PIC32_USE_PIN10_FOR_M1_PWM
#define MICROSTEPS 16 // 8 or 16
// For PIC32 Timers, define prescale settings by PWM frequency
#define MOTOR12_312KHZ 0 // 1:1, actual frequency 312KHz
#define MOTOR12_156KHZ 1 // 1:2, actual frequency 156KHz
#define MOTOR12_64KHZ 2 // 1:4, actual frequency 78KHz
#define MOTOR12_39KHZ 3 // 1:8, acutal frequency 39KHz
#define MOTOR12_19KHZ 4 // 1:16, actual frequency 19KHz
#define MOTOR12_8KHZ 5 // 1:32, actual frequency 9.7KHz
#define MOTOR12_4_8KHZ 6 // 1:64, actual frequency 4.8KHz
#define MOTOR12_2KHZ 7 // 1:256, actual frequency 1.2KHz
#define MOTOR12_1KHZ 7 // 1:256, actual frequency 1.2KHz
#define MOTOR34_312KHZ 0 // 1:1, actual frequency 312KHz
#define MOTOR34_156KHZ 1 // 1:2, actual frequency 156KHz
#define MOTOR34_64KHZ 2 // 1:4, actual frequency 78KHz
#define MOTOR34_39KHZ 3 // 1:8, acutal frequency 39KHz
#define MOTOR34_19KHZ 4 // 1:16, actual frequency 19KHz
#define MOTOR34_8KHZ 5 // 1:32, actual frequency 9.7KHz
#define MOTOR34_4_8KHZ 6 // 1:64, actual frequency 4.8KHz
#define MOTOR34_2KHZ 7 // 1:256, actual frequency 1.2KHz
#define MOTOR34_1KHZ 7 // 1:256, actual frequency 1.2KHz
// PWM rate for DC motors.
// Note: for PIC32, both of these must be set to the same value
// since there's only one timebase for all 4 PWM outputs
// Bit positions in the 74HCT595 shift register output
#define MOTOR1_A 2
#define MOTOR1_B 3
#define MOTOR2_A 1
#define MOTOR2_B 4
#define MOTOR4_A 0
#define MOTOR4_B 6
#define MOTOR3_A 5
#define MOTOR3_B 7
// Constants that the user passes in to the motor calls
#define FORWARD 1
#define BACKWARD 2
#define BRAKE 3
#define RELEASE 4
// Constants that the user passes in to the stepper calls
#define SINGLE 1
#define DOUBLE 2
#define INTERLEAVE 3
#define MICROSTEP 4
#define LATCH 4
#define CLK_DDR DDRD
#define CLK 4
#define ENABLE 7
#define SER 0
#define SER_DDR DDRB
// Arduino pin names for interface to 74HCT595 latch
#define MOTORLATCH 12
#define MOTORCLK 4
#define MOTORDATA 8
class AFMotorController
void enable(void);
friend class AF_DCMotor;
void latch_tx(void);
uint8_t TimerInitalized;
class AF_DCMotor
AF_DCMotor(uint8_t motornum, uint8_t freq = DC_MOTOR_PWM_RATE);
void run(uint8_t);
void setSpeed(uint8_t);
uint8_t motornum, pwmfreq;
class AF_Stepper {
AF_Stepper(uint16_t, uint8_t);
void step(uint16_t steps, uint8_t dir, uint8_t style = SINGLE);
void setSpeed(uint16_t);
uint8_t onestep(uint8_t dir, uint8_t style);
void release(void);
uint16_t revsteps; // # steps per revolution
uint8_t steppernum;
uint32_t usperstep, steppingcounter;
uint8_t currentstep;
uint8_t getlatchstate(void);

Any help is greatly appreciated, and if I missed anything please let me know.
I will be sure to share the code after I get the robot up and running. The only thing stopping me from continuing is the motor 1 issue.