I couldn't budge any of the nuts when I was doing my headers. I soaked them all with PB Blaster and kept working on them slowly until I got them free. I actually removed all 6 studs from the block... I only got the nut free from the flange, not the stud. So all 6 studs came rigtht out for me once I broke the rust.
If you cannot get the nut free from 2 of the studs, I would try BP Blaster (any auto supply place should have it) and slowly work on turning them until they break free. If you just cannot get the studs out of the engine block, I'm not sure. You could probably back 2 nuts against one another and use an open ended wrench to turn it out, maybe using some PB Blaster to assist. But if the threads are in okay shape on those, you can just reuse them.