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1) My Flash is a bit rusty, but high quality music files lined up against the Flash file tend to produce best results. .ogg and .wave could be considered, but maybe the new Flash suites can better sync up with .mp3.
2) Flash-ripping mostly. Get the original flash file, work it out to its base, and then at some point just insert the music and the graphics for most jarring, hilarious effect.
3) My guess, clever use of Vegas Pro sound editing and video fragment editing. And a good ear for music and notes, besides.
Question back. What's that anime?