So no one has quite come out and written the story where Harry and John are dating, and John just cannot cope with what he perceives as Thomas the ex.

Something like it was written wonderfully for laughs in the first round, but what I'm after is the serious version. Where Harry keeps telling John to let it go, but John just can't because he's exactly that obsessive about every aspect of Harry's life. And seeing the way Harry and Thomas know how to hurt each other, all their little in-jokes, the way they can be really sweet together, how it tears Harry up when they have a falling out just drives him absolutely crazy and he can't leave it alone, even if it pisses Harry off and forces him into a really bad position of split loyalties.

Whether/how John finds out the truth is up to writer.