2) A few of the sections on the DVD seem to have two audio tracks. Is there any difference between the two?
The second audio track was used to save disc space on some of the special features ... an extra audio track was used for Garrick Hagon's extended interview, and for the two different versions of Lapti Nek.
3) I know it's impolite to bitch about a fan made work such as this, but why did you "burn in" the explanitory notes rather than placing them in the subtitles? I wouldn't usually mind - but on a few occaisions the subtitle stream overlaps with the on screen text!
The explanatory notes are burned in because the film is not intended to be viewed without them. Without the notes, certain scenes would just be showing what the final film already does! Also, the burned in subtitles look better than DVD-standard subtitles.
I avoided putting burned-in notes on the deleted scenes such as Biggs and Jabba, so you get "extra notes" appearing on the subtitle track. In some cases, the scene being subtitled was so short, that to make its notes readable they did butt up against the burned-in subtitles a little bit.
Still, better than no notes.