I can recommend some general d3 resources I've found helpful (some of which you've probably already found, if you've been looking).
For a real step-by-step, the series of tutorials by Scott Murray look quite good, though I've not done them myself. I have done a MOOC with Scott as an instructor and I can vouch for his teaching skills. I think they'd be very useful for someone very new to HTML/CSS/JS (I'm not sure if that describes you) who also wants to start with d3 at the same time.
If you want to dive right in, I'd start on Thinking with Joins and How Selections Work, and for a practical example of those concepts, check out the General Update Pattern examples (one, two, three).
Once you think you've got a general grasp of things, I'd recommend looking through the examples for something that piques your interest and start pulling it apart to see how it works. That's the beauty of web development—it's pretty easy to find out how something is done because it's not locked away in a compiled executable.
Aside from that, read the documentation carefully. It's easy to miss details when skimming it because you want to get something done, but everything is there. It's excellent documentation.