I’m the one who made that rip, so I’ll answer that question. 🙂 As far as I know, the other tracks I neglected to rip, due to the inability to remove sound effects were the "Boss Intro" themes.
Other tracks whose openings were shortened:
Mini-Game Start Fanfare ~ Ordon Goats
Twilight
Faron Woods
Diababa (2nd Time)
Surrounded by Fire
Horseback Battle
Fyrus
Giant Twili Parasite
Lakebed Temple
Great Deku Frog
Morpheel (1st Time) ~ Argorok (1st Time)
Arbiter’s Grounds
Stallord (2nd Time)
Blizzeta (1st Phase)
Armogohma (1st Form)
Hidden Village
Celestia, the City in the Sky
Morpheel (2nd Time) ~ Argorok (2nd Time)
Hologram Zant
Tracks which were impossible to rip sans sound effects:
Summon Epona
Open Treasure Chest
Catch Item Fanfare
Catch Small Item Fanfare
Monkey Pursuit
Dark Grotto
Training
Down the Rapids
Zora’s Domain
Queen Rutela
Up the Waterfall
All Eight Wolf Songs
Sacred Grove
Statue Guardians
Gerudo Desert
Tracks which suffered from both problems:
Ordon Ranch
Practice
Tracks with omitted segments:
Taming Epona
Combat
Diababa (2nd Time)
Sumo Wrestling
Hyrule Castle Town
Battle with Zant
Final Battle – Dark Lord Ganondorf
Hope this helps.
-Jon T.