Hi evrl,
I removed your reference to me in your post. When you do that, it often deters others from responding and they may have some advice too.
I personally have never done any major modifications with my template (as you can see) but any time I have a question, I go to vbulletin forums and those people there are extremely helpful. I can understand what you're going through, though. I was overwhelmed at first but just kept playing around until I figured things out.
But check those forums and ask questions there too. There are some people there who REALLY know their way around the software and have done some amazing things.
http://www.vbulletin.org/forum/index.php