Module or not to module?

I've hit a rather large brick wall on this one. I have created a whole unit using the files and folders model. (incidentally trying to explain the difference between using files and folder AND learning modules is nearly impossible to non-users). Anyway, using this method provides a very courseware like interface once you get into a particular weeks entry. This will consist of a page (actually a folder) which has text explaining what is happening that week (learning outcomes etc) and below will be a series of linked files. These may be lecture slides, handouts, web links and/or links to Learning Modules (eg. Learning modules on Academic Writing, Time Mangement or Plagiarism).
The biggest downside to the model is that the main text for each weeks entry is held in the header of the particular folder. Whilst this is accessible and easy to edit I can't help feel that we are forcing the header to be used in a way it was not intended.

So the alternative. Create each weeks entry as a Learning Module. The text for that particular week is created in a separate html file and is attached as the first document. Subsequent files such as lecture slides are also linked and appear in the learning module menu. There is no indication of the file format (or size) so this will need to be added manually.
So far so good. The problems. Now that we have created 24 weeks as learning modules, each of these weekly entries now appears under the learning Modules button in the Course Tools menu. But our weekly entries aren't really learning modules, but they are now mixed up with the 'real' learning modules on Time Management etc.
Also, we can't link to a learning module (eg. from Week 2 to the Time Management module) from within the week (because learning modules can't link to other learning modules).
Navigation is also poor in our current setup as the Course Tools menu minimises by default as you enter a weeks entry.

Basically both options are a 'bit rubbish', but which one do I go with. I lean towards the Learning Modules option because I like more than anything the idea that each weeks text is held on a discreet web page as opposed to in the header of a folder.