Make it in a single text thread.
What version of InDesign? While things have gotten better, from what little I know of accessibility, even following every procedure you should in InDesign still forces some clean up work in Acrobat.
I'm using the latest versions of all of Adobe products.
One thing that helped me was checking off "Use for reading order in tagged PDF" in the flyout menu of the Articles panel. This has ordered the content in the Tags panel in Acrobat. HOWEVER, the Reading Order panel in Acrobat is still not correct and does not follow the article order I have assigned.
I suppose I could do "clean up" work in Acrobat, but my document is 28 pages and quite complex, and there is no undo button when reordering content in Acrobat. And if I need to update the PDF file I will have to go through the reordering process in Acrobat all over again - which would take many hours.
I also tried reordering the items in the Structure pane to see if that helps but it does not.
My stories are all threaded properly.
The Reading Order panel in Acrobat is set by the Layers panel in InDesign. It goes from bottom to top (i.e., the layer on the bottom is at the top of the reading order). Setting this can be very tedious, but it is still easier than remediating it in Acrobat.
Using the layers panel to set the reading order can cause a problem if you have text that is layered on top of a picture, but for some reason need the text to be read before the picture's alt text (like if it's a heading for the picture). I don't have a solution for that other than to avoid it or ignore it.