I wouldn't remove the intake manifold. I'd go crazy with a pressure washer.
They make this stuff for spraying on your rose bushes to keep deer from nibbling on them. It tastes horrible. (Ask me how I know.) I bet it works on mice too. You might try to find something like that. Sprinkle minced onions, or dowse the engine in pepper spray, or both. If they don't get the message, try-mouse paper. Yes, it works like fly-paper. Lastly, park your car in a garage and leave it running for a few hours.
The only downside to carbon monoxide is that the little buggers will probably die inside your heater vents. Not to worry though, the smell goes away in a few months, and air fresheners disguise rotting corpses pretty well.