Hi Vinny,
Scott offers two good suggestions which you should look at.
Thanks for the link. We do much the same thing in a training environment. It is all about transitions from one presentation medium to another. I went to >
http://www.reviseguys.com/moodle/mod/resource/view.php?id=96
Edexcel AS/A2 GCE in Chemistry. That is a huge course and you are weaving elements of Moodle into it. Nice. I randomly selected the topic:
1.2 Formulae, equations and moles.Essentially the Moles workbook is a big lesson. It presents pages of materials (branch pages that are grade netural) It has excercises which are a series of questions. It is broken into 12
sections which are classic branches.
The problem with the Mole book is that a student will have to remember where they stopped, or print it up. There is no immediate interaction with the student after a question. You can't send them to the page that contains the answer, or provide some feedback through a responce.
Of course bringing this into a lesson requires work. I offer Moles as an example of a lesson that should help you when you read what Scott suggested.
Somewhat related, I also think that your "calculate your empirical formula" is an assignment in Version 1.6. It is possible that it is only a fun assignment, so a netural resource works for you. Did not go into the first quiz but wondered if this should be a series of questions in a lesson. The last quiz is probably a "test" and thus a quiz in my book. These comments are not from an educator.
I realize that your site may encourage peer interaction rather than teacher interaction.
Hope this gives you some more specifics to think about.