It takes a significant amount of effort to do this all personally, this is very commendable. I self-publish and work for a company that helps others self-publish by editing/designing and converting their work, and it's always something very involved.
It's not as simple as just clicking convert either. Tables render differently in Epub and kindle, TOC creation can be a veritable mess and table rendering in Epub and Kindle conversions look different if done wrong.
Mobi conversion tools may or may not fix issues that'd appear if the official Kindle KDP tool is used, meaning a converted Mobi may end up looking entirely different than the same file once uploaded to Amazon.
Graphs... I don't even want to think about dealing with those and Kindle, congratulations on doing all of this yourself without screaming. My first couple book conversions were learning experiences, and they were mostly plain text (chapter fiction books) without varying fonts and diagrams.
So, if I had to sum up what I've learned into one idea that'd make the entire process easier, it'd be this:
Write plain text or rich text. Don't format when writing. Do write as non-fancy as possible in your master text. Then when you have to add stuff to it later, you don't discover little surprises that throw everything off.
For example: Don't indent. Kindle auto-indents when converted if indentation hasn't been defined in the style. (The official Kindle will, and only currently, who knows if it'll change in the future, and a Mobi generator generally doesn't.) So using TAB indents throughout a book instead of MS Word's feature will cause a massive headache just when you think you're done.
Since I work on Windows, the tools can be rather simple. Create a document in MS word. Save as a web page (filtered) - to remove some of the junk word creates in html. Edit the html to remove a couple other quirks, set tags for chapters, remove unicode that Kindle won't recognize (some are, some aren't), save, convert, and check what you missed. The less special your document has to look, the easier it'll be.
Again, congratulations, welcome to the world of self-publishing. It can give a nightmare of a headache, but once it's done, the joy of knowing you created something on your own is magical.
Thank you :) Yes! "magical" is a great way to describe the experience...
As you suggest, I tried to keep things simple with the text, but in the end since I use a lot of code samples and diagrams it was difficult to do that. And yes, rendering graphs was also a challenge. I didn't get into those details in the blog post, so let me know if anyone is interested in hearing more about that.