I'm not clear from your posting whether the Flash will be replacing traditional Moodle navigation or whether it takes over a level or two below within a stand alone Moodle course?
On a separate note I had a look at your course and there are some nice ideas here. I used to work with Becta and ran some elearning subject training days for A level sciences. Have you come across the resources on Becta's Ferl site (http://ferl.becta.org.uk/display.cfm?page=419) ? These include a range of low tech interactivities eg using Excel creatively for enthalpy experiments or PowerPoint animations for Bornhaber cycle. Thought there may be something of interest there. See also Mike Docker's site
http://www.mp-docker.demon.co.uk/home.html (if you've not coma across it before.