Try welding. Put a nut on the stud and weld both together through the nut hole. Usually the welding heat burns the rust, heats the metal, releases the threads, so after the welding in most cases the stud can be unscrewed with the nut.
Of course, once in a while this does not work, the stud or the weld breaks and then the option is to drill it. If the threads are bad/corroded or get damaged during the drilling and stud removal, you can put a special spring coil inside, which replaces the threads and lasts forever. Can be drilled even by hand, but the best would be using a milling machine. Another option - erosion, but you would need to locate a special shop where they do the job.
I would not recommend using an extractor tool /on a manifold/, too often the result is broken extractor in the stud, which then brings the need for super hard drills or electro-erosion.
