Lyric discussion by effington 

There's certainly more than just one person to consider in this song. You've got the musician who actually wrote the "pop song", and then the "girl" who "brainwashed" that person as well as some other unknown victim(s) of brainwashing ("she's brainwashed you too"). Then there's the songwriter's wife and another intimate companion -- I hear the last verse as "in '94 getting blown in your basement (while your wife slept)." So a whole cast of characters in this musical soap opera.

BTW, going by the track listings on Way to Normal and Stems and Seeds, the official title of this song is "Brainwascht", while the "fake" version kept the spelling "Brainwashed", rather than the other way around.

You raise some interesting questions, but I think the cast of characters is not as vast as it at first seems. The comment by AHoyBobby really sums up the backstory of this song, which puts the entire song into context.

The woman who brainwashed John & Flemming is of course, Frally, Ben's now ex wife.

I believe the correct lyrics would be "She's brainwashed you two," (instead of "you too") -- thus meaning that she (Frally) has brainwashed the pair of them (John & Flemming).

An error occured.