It seems like your saying that the studs have an unthread section up against the manifold. This is common when the stud has two different thread pitches. If so, I would think you would remove the offending studs and replace with the correct length and pitch that mates to the manifold. Nuts to match the thread pitch would be no problem and who is going to know.
I would try to remove the old studs with two nuts (jam nut) and use "Kroil" oil and be real slow by working the stud back and forth. Sheared manifold studs can make grown men weep.
