Super 6....can't put it off any longer. manifold questions

Your old studs have been through 10,000 heat cycles and are brittle. New studs would be tougher, but yes, there is the risk of breaking them trying to remove them. I was successful leaving the studs and using the Felpro gasket plus Hylomar aerospace gasket sealant. Since you are using new manifolds (new to the car) you should loosely bolt together the intake and exhaust manifolds (very loosely, just so they don't fall apart) and stand them up on the head mating surface on a known flat benchtop, and check that the flange thicknesses match at every position. I had to file several flanges where one was thicker than the other, so that the triangle washer would only have been pressing on the thicker one (or it would have cocked, locking that flange in place -- see below) -- this would have caused a manifold leak. You really want to perfect this as much as possible to avoid vacuum leaks, exhaust leaks, or both.

Here's the thing abut these super long six-cylinder manifolds -- you cannot use a thicker gasket to compensate for an irregular surface, like you might be able to do in some other scenarios. Because of thermal expansion, they actually need to be free to slide in the front-to-rear direction -- that's why the torque spec is so tiny. Anything that keeps them from sliding will probably cause a cracked manifold, and any irregularities in the mating surfaces or uneven torque will cause a leak.