That's pretty much the same conclusion I've come to. Snce I have a set of replacement manifolds already on the new engine, I'm thinking it's best to cut the old manifolds just above the flange clamp.
Well that would have been even an easier way out, as long as the manifolds are the same, you don't even have to change the gaskets. Although I don't know how much room you have, the other option is to unbolt the manifold from the head and go from there. That way you can address the affected bolts with the engine out of the way.
But a sawsall does wonders....