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(Thinking slowly today so am writing each of my points separately.)
I would urge Obama and friends to try their hardest to prosecute George Bush for war crimes. Why not? Just because it would mean a fight? The fight would elucidate what we are all about, and show up the resisters for what they are all about.
Second, How about using the threat of prosecution of Bush (rather than just an investigation) to help him see the folly of a blanket pardon of any kind? Why not confront him in person with this and somehow negotiate it? (Not offering to take investigation of him and his cronies out of the mix at any time.)