There really isn't any secret to dealing with rusted hardware it just sucks. Soaking in rust penetrate, using a torch, slightly tightening/loosing back and forth.
If the rust is so severe its eaten away at the fastener to where its an in between size you really just ought to cut it with an angle die grinder and some metal cutting disks. Shave the fasteners flush with the exhaust flange and force it apart.