This isn't the complete answer but see if it gets you in the right direction.
Basically you can change the audio.src via javascript. So I just replaced it with an object property that changes when the user clicks the next button. The first src defaults to the initial src of the audio tag. You can modify the code if you like but I figure it might be fine as is.
var allQuestions = [{
question: "Identify the musical interval",
choices: ["3rd", "5th", "4th"],
correctAnswer: 2,
audioSrc: " defaults to the original .ogg file"
}, {
question: "Which of the following best describes this chord?",
choices: ["Major", "Minor", "Diminished"],
correctAnswer: 0,
audioSrc:" http://en.wikiaudio.org/images/b/b8/MPC60_626_Cym_da_China_.wav"
}];
Then
function nextQuestion() {
updateScore();
questionCount++;
showScore();
showQuestion();
var audio = document.getElementById('myAudio')
audio.src = ( allQuestions[questionCount].audioSrc);
}