This is directly addressed in the GPL FAQ item, "Is it enough just to put a copy of the GNU GPL in my repository?"
Just putting a copy of the GNU GPL in a file in your repository does not explicitly state that the code in the same repository may be used under the GNU GPL. Without such a statement, it's not entirely clear that the permissions in the license really apply to any particular source file. An explicit statement saying that eliminates all doubt.
[...] lawyers and courts might apply common sense and conclude that you must have put the copy of the GNU GPL there because you wanted to license the code that way. Or they might not. Why leave an uncertainty?
For the past:
The question here is whether your GPL grant did in fact apply to the stories, even though you didn't mean for it to apply. This may come down to exactly what you said in your project (e.g., in your README, code headers, and any other license grant you might have specified external to the project) and possibly how the poject was structured (e.g., were the code and stories in separate directories? where was the text of the GPL, relative to these files?).
Merely placing a copy of the GPL alongside a creative work without explanation doesn't license that work under the GPL. Or does it? It is exactly this kind of legal ambiguity the FSF hopes programmers will avoid by including an explicit license grant within each file of a GPL-licensed project.
If someone did create a derivative work based on your stories, and you sued them, would the court rule that you did in fact license your stories under the GPL, or would they rule against the downstream recipient and say that you didn't license your stories under the GPL after all? I don't have a working knowledge of relevant case law (if any exists), so the answer to this question is not clear to me.
Note that you have indeed ceased distributing anything under the GPL, so only recipients of the old, possibly-GPL-licensed version of your work can make any argument that they have a GPL-licensed version of the stories. Certainly no one can correctly say, "You used to distribute this under the GPL in the distant past, so I'm going to pretend that my recently-downloaded copy is as well." However, people who genuinely do have an old GPL-licensed copy can legally distribute the GPL-licensed parts (whichever those may be) without issue.
For the future:
Simply be explicit about what parts of your project are licensed in what ways. Have a README or LICENSING file that says something like, "Files under the
foo directory are under the GNU GPL, version 3 or (at your option) any later version. Image files under
foo are also available under the MIT X11 license. Files in the
bar directory are made available only for personal reading and are all rights reserved." Now there's no confusion at all about which files are under which licenses.
The FSF also strongly suggests that you notate each individual file with what license it is under](https://www.gnu.org/licenses/gpl-faq.en.html#NoticeInSourceFile), since a README file can be separated from the licensed files, e.g., when someone reuses a particular file in a separate project.