First get a can of PB Blaster at the store it is the best stuff on earth for this sort of thing. Next you need a small propane torch like a plumber uses, a kind that has a push button start is convenient. Sounds like you went to far without those two importnat tools but atleast you will have them next time. You heat, spray and repeat and since I started doing that I have nto had a problem even with New England rusted fasteners. The next thing is 6 point sockets. If you use 6 point you cant round the fastener. 12 point sockets are convenient but as you can see lead you into some trouble.

JB weld and related products are not designed for heat over 500F so I would not advise using any type of chemical sealant. They really aren't designed to hold to things together without a lot of surface area and I'm assuming this is on one of those one holed flange things.

Last you need to say what engine you have so people who are familiar with that setup can comment.

Its not a GM engine cuz theres no pipe. maybe a 3.2 or 3.5? Is the fastener stuck in teh manifold with easy access? Google search "easy out". Or worst case scenario replace the manifold. If this is a 2.6 that is in the head right? Not familiar with that engine to comment.