Break the problem down! I suggest you forget about reading from HTML for now, and try to construct a minimal script that does nothing apart from write some IPA into an Excel file.

You can take as your starting point something like "h\x{025b}\x{02c8}lo\x{028a}" (your phonetic "hello" as a Perl string). That will completely rule out any possibility that something is going wrong at the HTML stage.

If you can get that working, you can easily plug it into your main program. And if you can't get it working, then it'll be small enough that you can simply post the entire script here, and we can try and help you figure out where it's going wrong.