If you don't already have TextWrangler set to do so, you may need to tell it to default-output any files you create as UTF-8.
Go to Preferences/Text Encodings and select Unicode (UTF-8) from the dropdown, and while you're at it, Preferences/Text Files should be set to Unix (LF).
It's possible KindleGen may be choking on Mac line endings or a Mac OS Roman-encoded file.
If this is the case, you can check the settings on your existing files by looking at the very bottom of the window, where you'll see a bunch of info which turns out to be dropdown menus you can change stuff with.
The other thing you might try is creating a new OPF from scratch. It's possible that while you think you might have changed everything over from your template, there could be something that was missed, and that could be holding things up.
Also, check to make sure that your NCX has no superfluous closing tags or even tags which don't belong in an NCX, e.g. a </navPoint> end-tag with no beginning or a <div></div>. That's another of the things that KindleGen is picky about and will silently ignore your NCX without even an error warning if it finds one.