Triggering GreyBox from within a flash movie? (link rel question)

I am working on a project that requires an animated intro for a website. The intro seamlessly animates into the main interface, where there are three distinct categories. The links to the categories are also animated, as three objects floating in water.

I would like to use these three links to trigger three different sections of the website, but in order to make life easy on the recipient of the website, I'd like to make those three pages either flat HTML files or pages created through a CMS system such as Wordpress of OpenCMS or something. (This is not the important part, I'm sure we'll come to some agreement on how the actual content will be managed.)

I would like, however, to keep the intro/menu movie constantly running under the popup AJAX 'window' so that there is no back-and-forth page loading. However I am reading online about link rel not working the way that I assumed it would, and many people asking questions about it. I do not know Javascript well enough to start recoding anything.

What would be the most straightforward way to call a Javascript function from within Flash? I have found the following site ( http://blog.codefidelity.com/?p=18 ) in my preemptive research, but it specifies LightBox. Will replacing the JS library (or whatever) work just like that?

The second part of the question is this: I need to make the links loop, because they're animated. However, I have never been able to do this in AS3.0, and only know as far as GoToandPlay for looping. At the same time, I need these three identical movies to start playing a few seconds apart from each other so that they don't look too monotonous. How does one trigger separate .swf files inside of a .fla project without having to play out the whole animation manually? I really have no experience with AS3 and only know enough 2 to get around very simple animations. However, I now have access to the whole CS4 studio, and want to make my time on it worth it, so I do not want to revert back to AS2.

thanks for reading, thanks in advance to any and all suggestions. If anything needs to be clarified just ask.

-Tim