Clean the mating surface with a chunk of red ScotchBrite. It's abrasive, but softer than the aluminum so it won't scratch the surface. It does a better job of getting into irregular places as well.
I wouldn't worry about the bottom of the crankcase. Clean the mating surface and let it drain for an hour. A quick wipe with a paper towel with a little fuel on it just before assembly should have it clean enough fort he sealant.
For the bottom of the oil pan, I would just give it a wipe with a couple paper towels to mop up any oil or dirt on it, and then let it soak for 10-15 minutes in some hot water and Dawn dish detergent. Dawn does a pretty good job of cleaning oil muck off of water fowl and oil pans. It's also less toxic than almost any other alternative.