DEVELOPMENT OF NEW CONTENT ORGANIZATION STRUCTURE

The goal of this web design is to deliver a complex collection of related information in different combinations of related theme groups, so that the user can see how content is related and is different across different catergories.

I'm having a hard time figuring out how to put together the mechanics of the site, which at this point is more important to me than the actual content of the site.

The goal I have for this site structure is pretty complicated, so I've prepared a diagram of sorts to communicate what I have in my head.  Take a look:

http://stemler.org/stemler/Development/StructureDesign.pdf

If you have a minute, take a look at what i've got.  If you have any ideas or advice (or questions) about how I might get this to work, please share your ideas.
g s t e m 1 (@) g m a i l . c o m
Also pass this along to anyone you think might be able to help.

Specifically, I'm trying to figure out which languages are best to code the site (PHP, XML,  HTML, etc)
and also tips on how to use these languages together.

In reality, this is a big job for me and my skills are not too advanced, but I'm willing to try on my own, and also interested in possibly colaborating, or even paying for some of the basic framework to be done.