If the manifold studs come out easily enough that would make the gasket cleaning job easier, however they're usually a bit stubborn to remove so working around them is better than risking damaging the threads etc if they're tight.
You can carefully use a razor/scraper blade etc to remove the old gasket remains.. But go slowly and don't dig into the cylinder head as its only aluminium.
If there are any really stubborn areas you can use brake cleaner to help remove them. Or even a tiny smear of engine oil left to soak in for half an hour or so can help soften baked gasket material. Just remember to clean it off properly with brake cleaner when you're done.
You should be able to get the catalytic converter gasket off just using a scraper blade too. They normally come off in one piece if you carfully get the razor/scraper blade underneath it.