I don’t know if this is by popular demand or if many will find this useful, but here are two screencasts of what I do to clean up and format manuscripts of almost all types (pictures books are the only exception).
Click “Watch on YouTube” for best scaling options. (I suggest 720p).
I think everyone should do the first video. The second is as needed and as you find it useful. Questions in the comments or on Twitter @andrewkarre.