I wouldn't bag anything, unless you can get it completely dry first. Otherwise it might mildew or harbor some stinky microbes or something else unpleasant. Maybe throw a sheet or something over it to keep dust, etc. out of it.
As to the substrate, a few months back I tore down a tank with flourite and dirt. It was kinda a mess, but I went through several cycles of drying the substrate (a thin layer in several different buckets), and then winnowing with old tank or driftwood-soaking water. put the water in, stir the bucket up good, and pour off anything floating/suspended. A few of those seemed to remove most of the dirt (although it did leave sand and rocks/gravel from the dirt behind).
As to the media, I'd just rinse it out good and let it dry, most of that is pretty inert stuff, so I don't see why not reuse it.