I'd just like to say, "Prove me wrong" is in the thread title. >_>
Ok, first off, completely ignoring the fact that it will be nigh impossible to have the magnet and plane support each other, the system has no way to change the amount of magnetic power emitted in a reliable manner, without completely destroying the balance of the plane. Thus, by adding a reverse thrust, one of three things can happen, assuming we ignore the unwieldy nature of the setup.
If the magnets are of equal power, it will cease movement in either direction.
If the rear magnet is of greater power, the vehicle will move only in reverse.
If the rear magnet is of lesser power, the forward motion of the vehicle will be slowed.
On this same concept, assuming the magnet above the chassis actually lifted the plane, it would continue to do so, as there is no given method to turn it off. Before long, your aircraft would become a spacecraft.
Pulleys. Very inefficient. Assuming you can actually work them in a reasonable amount of time without them catching, thus eating precious time, you'd need to modify the positions several minutes, if not tens of minutes, before you needed to be at a certain speed or altitude. Hours for larger changes.
The magnet support is to thin and weak. The top magnet, if strong enough to actually lift the plane, would bend its support, thus causing the magnet to touch the plane and never acheiving liftoff. The front support would break in a similar manner, as would the rear.
Now, even if you managed to somehow get all the rest to work, it would be EXTREMELY un-aerodynamic. Travel times would be monstrously slow, and air resistance would pull the vehicle apart over time.