Someone here offering a "step by step guide" is essentially the same as offering a tutorial, but with way more work involved.
The reason everyone on here says "here's a starting guide, go try it" is that that's how most of us learned, especially php.
So, this is exactly the answer you asked to not receive, but the absolute best method for learning is to have a goal in mind, and then build it.
Can you comment on this answer with a small project in mind? I'd be more than happy (or maybe other people too) to help get you started. But, I cannot tell you how to rewrite StackOverflow. I doubt the answer would fit in this text box.
Come back with "I want to rewrite Digg" or "I want to share recipes with friends" or something like that, and we can help you.
Edits based on comments below.
If you want to make a site like Craigslist, let's focus on one area for now.
Plan it out. What does your final product look like? Remember, you don't want replication of data, so think about what groupings of data you'll need. Things like categories, users, and posts, if we're keeping it simple.
You'll need to create a CRUD (Create, Read, Update, Delete) for each data group. This is a place to create categories, users, posts, view them, edit them as needed, and remove them.
You'll also want to connect these things together. So, for example, in a table of posts, you'll want a field called category_id or something, with the row id of said category. Then you can easily link posts to categories, view all posts in a category, etc.
What is your understanding of connecting to a database, retrieving results, etc? If this is completely over your head, I would definitely advise getting a book like the other answer suggests.