It'd be a rather grand undertaking in and of itself to redo the actual music for the opera. As Covarr said, we already have the redone music from the OCRemix album, the problem is entirely a programming one. Getting the time cues in the game to sync, not just the mouth flaps but the dialogue timings and the proper "you made the right choice, you made the wrong choice" stuff all working right is going to be a pain in the ass, as this is all stuff that the "new track" handler that we're overwriting in the game's code isn't used to handle, instead there's very specialized code in the game for handling that sequence musically.
This is the bit that's a pain, because we have to have our own very specialized code for this sequence. Our code for most other sequences is very simple and thus very easy to maintain. Dancing Mad and The Phantom Train are also going to need similarly specialized handling (though not as detailed) for only somewhat similar reasons.
To be honest, it's not quite accurate to say we're "still having trouble" with the Opera, though. Code-wise, I haven't even started with the opera. The way our code works, I can choose not to handle certain tracks and the game's native music code will handle it, so I'm having it to do that for the Opera for now, and haven't even begun the runs through the debugger required to set the stage for coding the opera stuff.
In other news, I've completed preliminary work on designing the installer, which is a vital step towards being able to get copies out to our alpha-testers.