Hi, for anyone that's still having the ID story or scrollbar issues, I basically just removed the <div id="story"> and </div> from the middle paragraph in the Story Interface passage so that only:
<span id="back" class="lnr lnr-chevron-left"></span>
<div id="passages"></div>
is left behind! I left the rest of the original code untouched (except for the config fix in javascript) so that the scrollbar was still functional!
I believe the issue is due to the sugarcube 2.37 update that treats the entire StoryInterface passage as if it's contained within the <div id="story"> container, so it doesn't allow the "story" element to be mentioned in the passage anymore. I'm not sure how this will affect the header and footer since I'm still new to twine but hopefully this doesn't break other parts of the game!
Also thank you to the author for the amazing template and everyone else who suggested fixes!