Hoi, I read this in digest mode so let me answer things together.
The reason why .ogg files are not great is because indeed it is a lossy algorithm. There is some great software to analyse pronunciation files; a program called "praat" is worth mentioning it is even licensed under GPL. There is even functionality in there to do with IPA transcription.
Gregory's proposal to use Ogg/FLAC is not helpfull. This is not the format that is used to analyse pronunciation files. The notion that a specific quality was "the gold standard" at the time is indeed that. It used to be, times have changed.
The Shtooka program that we are talking about CAN create both a WAV and an OGG file. It just needs asking. It would be helpful if we learn sooner rather than later what the outcome is of this request.
Thanks, GerardM