rewrote script, this works (kind of)...only issue is that it works, but doesnt disengage, and also seems to interfere with control of plane?? I am sure this can be cleaned up to work better, ideas?? I am new to scripting, but learning fast, thanks for the help!!

private var isBoosted : boolean = false;
private var normalSpeed : int = 1000;
private var boostSpeed : int = 2000;
var speed : int;

var gameObjectGUI           : Transform = null;

var explosion               : GameObject;
var splash                  : GameObject;

private var forceWingLeft   : Transform;
private var forceWingRight  : Transform;

private var forceTailLeft   : Transform;
private var forceTailRight  : Transform;

private var forceNoseLeft   : Transform;
private var forceNoseRight  : Transform;

private var forceThrust     : Transform;

private var thisTransform   : Transform;
private var thisRigidbody   : Rigidbody;

private var thisGravity     : Vector3;

private var myPitch      : float;
private var calPitch      : float;
private var offsetPitch  : float;
private var calibrationZ : float;

function FixedUpdate()
{   
    if ( iPhoneInput.touchCount > 0 )
        setCalibration();

    var accel : Vector3 = iPhoneInput.acceleration;

    if ( calibrationZ > 0 )
        myPitch = -Mathf.Atan2( accel.x,  accel.z ) * Mathf.Rad2Deg;
    else
        myPitch =  Mathf.Atan2( accel.x,  -accel.z ) * Mathf.Rad2Deg;

    calPitch =  ( wrapAngle( offsetPitch ) - wrapAngle( myPitch ) ) / 360;

    thisRigidbody.AddForceAtPosition( thisTransform.forward * speed, forceThrust.position );

    //Get the angle between our velocity and the front of the wing
    var angleOfIncidence = Vector3.Angle( thisTransform.forward, thisRigidbody.velocity );

    //Taking the Sin of the Angle of Incidence will yield 0 at 0 degrees difference
    //and 1 (representing full friction at 90 degrees). This is what changes the direction
    //of the plane's velocity vector.
    var wingFriction = 0.1 + Mathf.Abs( Mathf.Sin( angleOfIncidence ) );

    //Add a small amount to the acceleromter values if they are equal to zero
    var accelX = calPitch;
    if ( Mathf.Abs( accelX ) < 0.02 )
        accelX = 0.0001;

    var accelY = accel.y;
    if ( Mathf.Abs( accelY ) < 0.1 )
        accelY = 0.0001;

    var relativeLeftWingPosition  : Vector3 = thisTransform.position -  forceWingLeft.position;
    var relativeRightWingPosition : Vector3 = thisTransform.position - forceWingRight.position;

    thisRigidbody.AddForceAtPosition( thisGravity + ( -thisRigidbody.GetPointVelocity( forceTailLeft.position  ) * 0.1  ) + ( ( -thisTransform.up * 5 * -accelX ) * wingFriction ), forceTailLeft.position  );
    thisRigidbody.AddForceAtPosition( thisGravity + ( -thisRigidbody.GetPointVelocity( forceTailRight.position ) * 0.1  ) + ( ( -thisTransform.up * 5 * -accelX ) * wingFriction ), forceTailRight.position );

    thisRigidbody.AddForceAtPosition( thisGravity + ( -thisRigidbody.GetPointVelocity( forceNoseLeft.position  ) * 0.1  ), forceNoseLeft.position );
    thisRigidbody.AddForceAtPosition( thisGravity + ( -thisRigidbody.GetPointVelocity( forceNoseRight.position ) * 0.1  ), forceNoseRight.position );

    thisRigidbody.AddForceAtPosition( thisGravity + ( -thisRigidbody.GetPointVelocity( forceWingLeft.position  ) * 0.25 ) + ( (  thisTransform.up * 2 *  -accelY ) * wingFriction ) - thisTransform.forward * relativeLeftWingPosition.y  * thisRigidbody.velocity.magnitude * 0.0025, forceWingLeft.position  );
    thisRigidbody.AddForceAtPosition( thisGravity + ( -thisRigidbody.GetPointVelocity( forceWingRight.position ) * 0.25 ) + ( (  thisTransform.up * 2 *   accelY ) * wingFriction ) - thisTransform.forward * relativeRightWingPosition.y * thisRigidbody.velocity.magnitude * 0.0025, forceWingRight.position );

    audio.pitch = 1.0 - Mathf.Clamp( thisRigidbody.velocity.y / 100, -1, 1 );

}

function handleRaycasts( theHit : RaycastHit )
{
    switch( theHit.transform.name )
    {
        case "coin":
            Destroy( theHit.transform.gameObject );
            Debug.Log( "Collected a coin!" );
            break;

        /*case "water":
            var splashClone = Instantiate( splash, thisTransform.position, thisTransform.rotation );
            Destroy( gameObject );
            //gameObjectGUI.SendMessage( "crash" ); 

            var script : crash = gameObjectGUI.gameObject.GetComponent( crash );
            script.crash();

            Debug.Log( "Splash" );
            break;*/

        default:
            var explosionClone = Instantiate( explosion, thisTransform.position, thisTransform.rotation );
            Destroy( gameObject );
            gameObjectGUI.SendMessage( "crash" );
            Debug.Log( "Crash" );
            break;
    }   
}

function setCalibration()
{   
    var accel : Vector3 = iPhoneInput.acceleration;
    calibrationZ = accel.z;

    if ( calibrationZ > 0 )
    {
        offsetPitch = -Mathf.Atan2( accel.x,  accel.z ) * Mathf.Rad2Deg;
        offsetYaw   = -Mathf.Atan2( accel.y,  accel.z ) * Mathf.Rad2Deg;
    }
    else
    {
        offsetPitch =  Mathf.Atan2( accel.x, -accel.z ) * Mathf.Rad2Deg;
        offsetYaw   =  Mathf.Atan2( accel.y, -accel.z ) * Mathf.Rad2Deg;    
    }   
}

function Start()
{
    forceWingLeft   = transform.Find( "forceWingLeft"   );  
    forceWingRight  = transform.Find( "forceWingRight"  );

    forceTailLeft   = transform.Find( "forceTailLeft"   );
    forceTailRight  = transform.Find( "forceTailRight"  );

    forceNoseLeft   = transform.Find( "forceNoseLeft"   );
    forceNoseRight  = transform.Find( "forceNoseRight"  );

    forceThrust     = transform.Find( "forceThrust"     ); 

    thisTransform = transform;
    thisRigidbody = rigidbody;  

    thisGravity   = Vector3( 0, -9.8, 0 );

    setCalibration();
}

function Update()
{
    var hit : RaycastHit;
    var layerMask = 1 << 2;
    layerMask = ~layerMask;

    if ( Physics.Raycast( thisTransform.position, thisTransform.forward, hit, 10, layerMask ) )
        handleRaycasts( hit );
    if ( Physics.Raycast( thisTransform.position, -thisTransform.forward, hit, 10, layerMask ) )
        handleRaycasts( hit );
    if ( Physics.Raycast( thisTransform.position, thisTransform.up, hit, 5, layerMask ) )
        handleRaycasts( hit );
    if ( Physics.Raycast( thisTransform.position, -thisTransform.up, hit, 5, layerMask ) )
        handleRaycasts( hit );
    if ( Physics.Raycast( thisTransform.position, thisTransform.right, hit, 10, layerMask ) )
        handleRaycasts( hit );
    if ( Physics.Raycast( thisTransform.position, -thisTransform.right, hit, 10, layerMask ) )
        handleRaycasts( hit );
    if ( iPhoneInput.touchCount > 0 )
    {
        isBoosted = true;
    }

    if (isBoosted) {
    speed = boostSpeed;
} 
    else {
    speed = normalSpeed;
}

    /*if ( thisTransform.position.y < 0 )
    {
        var splashClone = Instantiate( splash, thisTransform.position, thisTransform.rotation );
        Destroy( gameObject );
        gameObjectGUI.SendMessage( "crash" ); 
        Debug.Log( "Splash" );
    }*/
}

function wrapAngle( angleToWrap : float )
{
    return 180 - angleToWrap;       
}

You seem to be setting isBoosted to false in every OnGUI call, which means by the time you query it in the FixedUpdate loop, it is always going to be set to false.

You should move the initialization of the isBoosted variable to your start function and remove it from the OnGUI function.