Not going to sound like the greatest idea but you might want to back off the other nuts a little, see if you can move the manifold just a little, then double nut the stud and see if that helps. It looks like the stud might be a little off-center in the hole and the manifold is jammed against it and holding the stud in. BTW, when you double-nut, put the wrench on the inside nut when you try and remove the stud
Also, make sure you're starting the right end of the stud in the hole. They often have more threads on one end than the other.