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The pronouns are handled not through gender. There is a prompt that says "Choose pronouns" you can also go through the settings and change your pronouns there. 

For the pop-up, are you using the itch.io app or the website version? Another person had this problem and it was more so due to the app than anything on my or the stories part.

Oh well now I just feel dumb..you're right, the pronouns do work correctly when I actually did click that prompt and change it, I don't know how I completely missed it when I was playing. I'm sorry!!

And I was using the app! But I'll just use the website version from now on. Again, thank you so much for your response and I'm sorry to have bothered you on a mistake that was on my end! 

No problem whatsoever, I'm glad you were able to fix it! :)