LadyDae, if your opf file is missing you are missing:
the metadata (factual details) pertaining to your publication
the entire manifest
and the guide.
This is a very significant part of the structure of your epublication. Epub generators such as InDesign produce this automatically (though InDesign inexplicably omits the date, which you have to go in and provide manually). What are using that no opf file was generated?