I think you've probably gone in the wrong direction. IF I were you I'll just focus on a secure wordpress installation with the necessary plugins, themes and I'll work on getting all the stuff needed for such a site and making it easy for them to maintain the products (user guides etc). Secondly you shouldn't be putting more hours than you should, it's not your problem.
Thirdly it's very reasonable to make your own ecommerce site but thats if you have platforms to use like wordpress, she is a startup and cannot afford proper development "obviously".
Edit: You've probably fucked yourself accepting this kinda job without talking to her properly about existing technology available and existing e-commerce sites that utilize these platforms. Put it up to experience