I highly recommend taking a look at
$1 as a first step. There are guidelines there for creating accessible documents. You are correct that all images should have alt text. For complex figures, you can also add long descriptions, which is basically text explaining the figure that lives in the main document and not in the alt text box.
I would avoid text boxes, extra line breaks, and the use of formatting as a means of communicating information. Screen readers can identify bulleted (unordered) and numbered (ordered) lists if you use the built-in list tools.
There are some differences in how screen readers function (the primary ones are JAWS, NVDA, and VoiceOver). Users can also adjust settings based on preference and that impacts how a screen reader will interpret content.
Once you gain some familiarity with the basic rules for creating accessible documents you'll feel much more comfortable with the process. Alternatively, you can outsource this task if you have a large number of documents to convert. Good luck!