[pblankenbaker]

Is it possible that your shooter takes more than 3.5 seconds to reach it's raised state? If it is mechanically OK to raise your shooter while you are driving you could start raising it at the start of auton at the same time as you start driving forward and let it run longer:

public void autonomous() { 
    myDrive.setSafetyEnabled(false);

    // Start driving and lifting the launcher immediately
    myDrive.drive(-.5, 0.0); 
    startRaisingLauncher(); 

    // Stop driving after 3.5 seconds
    Timer.delay(3.5);
    myDrive.stopMotor(); 

    // Stop raising launcher after 4.5 more seconds (8 seconds total
    // raising launcher)
    Timer.delay(4.5); 
    stopMovingLauncher();

    stopAll();
}

You should be able to use your buttons in teleop mode to experiment with how long the total time should be in order to raise the shooter (don't assume the 8 seconds shown in the example above is the correct value).

Good Luck.