Many thanks to the responders. I believe I have it fixed. I reinstalled and manually partitioned and only defined boot, swap, and / with all the rest of the space.
This will clearly get rid of the problem even though there are definite advantages to using more partitions.
The biggest error I made was reading the output of "Disk Usage Analyzer" as percentage of folder capacity instead of percentage of file system usage. It's so obvious now that I understand it. The documents for the Analyzer did not define what that column meant.
I spent 3 days trying to fix this on my own because I don't like to clutter public forums if I can figure it out myself. This was a last resort and I was thinking of giving up until I got all of your help.
Many thanks for being good citizens of the Fedora forums.