My favorite cheat to determine how well I've built an accessible PDF is to export it as RTF text.
That will maintain my text formatting, but let me know at a glance what is working and what is not. If the text doesn’t read cleanly, it gives me solid hints at where accessibility issues come into play and help direct me where I need to fix things to make it work better. It’s fast, convenient and telling. I always recommend this as the first place to start when trying to find random accessibility issues.
Please give it a try and see if it helps you with your issues.