The one which begins with "I am in receipt of a memo from some character using the pseudonym D.C. Fontana" (and then subsequently refering to the name D.C. Fontanta in quotation marks all the way through the rest of the memo) is one that always raises a chuckle from me.
There aren't any quotation marks around Fontana's name in that memo (see The Making of Star Trek
, p. 165). You may be conflating it with a memo referring to first-season story editor John D.F. Black, whom he referred to as John "D.F." Black and jokingly accused of ripping off Dorothy Fontana's initials. I can't seem to find the page that one's on, though.
Anyone have any further knowledge pertaining to the main title music being changed to eliminate the soprano?
All I know is what's on the CD set, which I believe is correct: the first season used the electric-violin version arranged by Courage followed by the cello version arranged by Steiner, and the soprano version arr. Courage was used in season 2 and again (in a new performance conducted by Wilbur Hatch) in season 3. So this seems to be a case where Justman & Solow simply got it wrong.