If the threads themselves are rough, you can do several things.
You can restore damaged threads with a special file known as a "thread restoration file". It has teeth at the required pitch and angle for specific threads. It files away the damaged parts.
You can also use a very, very fine lapping compound to grind the threads against each other. It will remove the high spots. You have to be very careful to clean out all the grit when you are done, otherwise it will continue to eat up the threads.
Daniel