I'd suggest using SWFObject to handle the IE click to activate problem. As for reloading the page, you could load subsequent pages onto your main page using the
IFRAME tag.
However, I would just toss it out there that maybe a Flash nav with the rest of the site content in HTML may not be the best way to go. Flash navs present some search engine optimization challenges and very often if you're dealing with an HTML site, having the nav in HTML ensures faster loading and no risk of a user not having the right version of Flash. Plus the usual rollover effects and the like which are done in Flash navigation can often be done in DHTML.
Believe me, I'm not dissing Flash (it's my bread and butter and I love it!), but sometimes it's not the best tool for the job.
Regardless, good luck and happy coding!
Best,
--eric