I have written a simple audio class wrapping riffwave.js by Pedro Ladaria. It should work in any browser that supports html5 audio elements including the wave format. I'll look into adding it into your project when i get some free time.
Could you explain the keyboard input issues? I'll see if I can help out (I worked on GWT based emulators and JavaScript based text editing/word processing, so I had to work around some issues before).
After my first quick look into the code I wonder if there is a reason for the "replaced" package, instead of using a "super-source"?
Also, I wonder what the steps are for setting this up locally, especially how to add files to the dos file system. I assume I have to create an image, but I don't know what kind and where to put it. (edit: I think I found it in the source. But a few words on configuration and loading the image (as well as creating it) might be a good addition to the read-me to help new people working with the code)