Nice catch on the README error, it's surprisingly difficult to type out "run".
As far as the GUILE_LOAD_PATH thing is concerned, other games I've made did have slightly better documentation in that regard, but it really ought to be documented as part of setting up Tsukundere. configure.ac is a good way of detecting broken setups, but not a good way of teaching the correct method. A thing that many people will get wrong because they don't care about it, is putting environment variables in bashrc. They don't belong there. Use bash_profile, profile or /etc/environment.
The current-window thing might be a bug of broken compile caches. I don't see you having set up GUILE_LOAD_COMPILED_PATH, so I'll have to assume everything gets autocompiled on first execution. Try cleaning $(HOME)/.cache/guile.
As for the choices it is basically the same incident but with a different perspective, depending on which set of Aya's lies factual reports you believe. It's set up to make you question the reliability of pretty much everyone involved as a narrator, so if you feel like you need more information on whether the X is actually harmful, that's exactly what it's trying to evoke. Though I guess for those who don't want to spin off fan fiction from fan fiction, that is not terribly satisfying, now is it?