Goodness, have you drug something out from under the carpet.
For CURRENT information on creating your own theme from scratch, and I don't recommend totally from scratch, I'll give you some good references and links.
But let's explain why not totally from scratch.
WordPress uses Templates as building blocks to stack together to create your final page. You will need to understand how all the pieces come together and Stepping Into Templates will help you understand that process. It's more than just CSS today.
Using Themes will introduce you to the concept of using Themes in WordPress and Theme Development and Designing Themes for Public Release will help you understand more how all the parts and pieces go together and what you have to keep in mind as you are working.
This is a LOT to know and the amount of stuff you need to know increases, so I and others here recommend that you begin with a Theme that "resembled" what you want in the end. It doesn't have to be perfect, but the sidebar should be on the left or right as you want it, and the header should be there or not, and so on. Just a passing layout familiarity. Then rip it apart and work from there unless you are an expert in CSS, and so much of this is redundant information.
Everything from the old wiki has been moved into the WordPress Codex and totally updated. http://codex.wordpress.org is the place to hit for all the information you need.
Here are some other resources:
Site Architecture 1.5
Stepping Into Template Tags
Blog Design and Layout