So i had a motor burn out. the coils are all black instead of copper and the drone crashed,  luckily only after takeoff of about 4 ft.   However, i noticed that the screws under the burnt out motor were not flush under the plastic housing, they were sticking up, and not square either, This may have been the rotor that took the brunt of the impact.   If i replace this motor, will i still be in trouble because of these not in alignment threads?   Notice how the thread on the left is clean, but the 4 threads on the right are jacked up.

I would install a new motor and see, but to be honest since you already have to pop the top I would bite the bullet and purchase a new shell as well.

The angle that the motors mount is deliberate.  With melted holes, the motor will probably no longer be at the proper angle.  Replace the shell.  

There are no threads in the plastic.  The threads are in the motor.

I've had a similar thing happen to me except in my case all four screws and screw heads pulled right up and through the melted plastic leaving four gaping holes where the smaller screw holes should be.  I was able to repair it by using my dremel to grind down and even out the motor mounts.  Then I used longer screws.  I used flat washers to keep the screw heads from pulling through and more flat washers as needed as spacers between the motor mount and the motor to even the motor out.  After that and some other repairs, the Phantom flew like new.  I beat my distance record a few weeks later.  

Eventually as in several months later I had another crash and had to replace the shell.  

If you try it be sure you get screws that are exactly the correct length.  Don't allow the screws to penetrate the motor too deeply.