You can hear the organ much clearer on the extended takes that form part of the bonus tracks to the Beach Boys Smiley Smile LP - there's bits where it breaks down and Brian instructs the musicians what to do. IIRC he says something about a motor being on for one beat and off for another which I thought was in relation to the organ perhaps? Can't find a youtube link to the track though. If you can find the track check it out as it wil give you more of a clue by hearing it more isolated.