Download
calibre - E-book management
then install the add-on FanFicFare in Calibre. To do so, click Preferences, next select plugin, select get new plugins, then find FanFicFare and install.
You can use Calibre with FanFicFare to download stories from a variety of sites, including here, at suffcientvelocity. Just copy the url of the first page of this thread and give it to FanFicFare, that will get you an epub of this story which you can convert to PDF with Calibre (although Calibre may allow downloading in a variety of formats, FanFicFare can only produce epubs. Again, this doesn't matter because Calibre lets you convert epubs to a variety of different file types, including PDF).
The resulting PDF will have a table of contents and such. I much prefer making a PDF of this story that way than trying to use AO3's download option.
You may have to experiment a bit to find the settings that you like, but Calibre/FanFicFare has served me well.