Dan --

Two years ago I wrote some command line tools for editing RIFF/WAV files.
You can mix, fade, silence fill, and chop files.

I have not looked at these since then, and I don't remember
the details about different file formats, but I will send them to you and
you can try them out if you want.  Untar and make.  There is a document
that describes how to use them.  Let me know if they work for you.

-- Al