Are you allowed to submit a fangame/a game that uses characters from an existing game/book/manga (provided it is free to download and you include a disclaimer that it is a fangame not endorsed by the copyright holders of such characters)?

That should be fine. But yes, please put disclaimers that it's a fangame and not official. Also, I'm unclear on whether fangames can be receive money or not, so it should be free as well (without tips).