As for a likely plugin that can do most of what you want, have you thought about trying the Content Pages (mod_icontent) plugin? It allows students to post questions and notes below the content. Notes can be private or featured. Questions can be public or private to the teacher/tutor only. Content is presented very similar to the way presentation slides are shown. The teacher can even provide quiz questions for a grade, but not every question type is supported. It also seems you can have as many pages of content as you want.
As for the Hot Question plugin, it would be interesting to modify the submitdirections field for it to allow for some "content". Right now it only allows text up to 255 characters long, but could be easily modified. Again, all the student input would appear below and a big limitation would be that it would not allow multiple "pages" of content.