The Blu-Ray mono track for the first season seems accurate, but the 2006 version of the main theme is used at least once, the "cello" theme is used where it shouldn't, and so on.
In terms of music, man, music! It seems you know of three instances (excluding the main/end title mistakes, as I still think the CD set clears that up now) where the actual music was changed in terms of the Blu-ray's mono audio track. Are there more and do you know them? I understand completely if you don't have the time to write everything you know out, of course.
Just...to have every note of music from the series available on CD and not be able to put it into place has to frustrate somebody out there, yes?