Just some thoughts how I would troubleshoot (TS) this

1. I would TS on a copy of the file to experiment on
   
2. What kind of Fonts are in a document? I would click the small arrow to the bottom right of the Home--> Styles, and from the list on the right, move down the list, and as my cursor scrolls over an item, I can see among other things the fonts for the style listed -- For a manuscript, you should be consciously using Styles
   
3. With Styles, I can easily make changes (for example, fonts) that sweeps through my document
4. Not spotting something obvious, I would do a total uninstall--if you decide this is an option, then read how on my Troubleshooting page below -- DON'T UNINSTALL WITH WINDOWS, because you will keep the problem (if it is a problem)
5. If you do a reinstall, do NOT click Yes for any updates -- Do this after you get your core Word working

Maybe my thoughts will help you some till someone else provides a quick fix