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Glad it was just a stud.

Drilling and using an extractor can work but if you break the extractor off in the stud then things get very troublesome.

I would suggest that you take the car to someone that can weld a nut onto the stud and back it out that way.

I never use a torque wrench on a manifold. I just snug them up a little at a time until I feel most of the "squish" is out of the gasket. I check them a few times after driving until they settle in.

They don't have to be super tight if your surfaces are reasonably flat and are using a new gasket.

When installing I leave the two bolts holding the intake manifold to the exhaust manifold loose and tighten them last.