There is not a flicker of evidence that Bach had anything to do with the "Toccata and Fugue in D minor" and a lot of stylistic reasons to suggest it was somebody else's work.

http://en.wikipedia.org/wiki/Toccata_and_Fugue_in_D_minor,_BWV_565

Don, you had the misfortune to be at college during a bad period for Baroque historical scholarship. People only started sorting Bach's attributions and chronology out properly after you left. This is not "nitpicking" and it isn't conspiracy theory either, it's mainstream musicology.