Drill exhaust manifold bolt - Remove head or not?

Can try tapping the off centered hole you have there. Have it predrilled to the proper taping size for 5/16". Careful cause if you hit the broken easy out . . .

Have had that happen and just retapped them off centered. Not ideal but can work. Install and seal the stud with high temp rtv and good to go.

Might have to cheat the exhaust manifold flange to keep the manifold In proper position.

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No to welding the exhaust cross over shut.

There are intake manifold block off gaskets available.

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Worst case senario, can always walk It over to your local engine machinist and they can Helicoil it for you.