Acapellas already exist for every episode. Just go here for them:
http://www.mlptf2mods.com/create/reference-materials.
If you want to know how to get the acapellas, you need a 5.1 surround sound version of the episode and some tools to extract the audio and split apart the channels. Vocals will be on the center channel while you can combine the front left and right channels to get the BGM. I use a took called MKVExtractGUI to extract the audio tract from a MKV file. The audio has to be AC3. I then use a tool called BeSweet (and a separate GUI called BeLight) to split the file into single channel wavs. It was a bit of a pain to get set up and I'm not 100% certain I can reproduce.
As for automation, I'll see if I can write something up tomorrow for you. But it basically lets you adjust project/plugin values during the course of a song (like fading in the volume of a channel).