I think I disagree with both of these comments re: the final clue. Spoilers below.
By the end of the game, a player should have worked out that a thunderclap sounds when and only when someone dies. There is a thunderclap during John's scene in 25-AT-1. John does not die after the thunderclap. Therefore, the player should be able to work out that someone else has died somewhere, and that any missing scene must be a 25- scene.
You are told Katherine is K in the preceding scene in 24-LI-1, when John has a conversation with her. That immediately marks her out as a K. She would be a very poor fit as 13, because the player should have already been taught that the deaths count backwards. Katherine could only be 13 if she was the death before Rupert. Indeed, the game explicitly relies on this logic - there's no way to find 01-ST-12 unless you make the inference that Rupert is 12 as the earliest death, since there is no other scene which refers to Person 12. Logically, Amelia (if she had had scene) would have been 13, and it would be highly confusing to have Katherine as 13. Equally, Katherine can't be 0 because she dies before John. Really, Katherine is actually "Person 1" by the usual schematic and John is the one who is misnamed, as strictly speaking he doesn't die from the thunderclap, but if you made, say, Katherine 1 and John J, the game would be far too easy (the player would immediately notice Person 1 was never mentioned).
As such, you should be able to work out that there's a 25-##-K scene.
Finally, once you realise it is Katherine, all the clues are provided for you to know she is in Wintercote and therefore that the missing scene is 25-WI-K. Changing anything else would just make it far too easy.
At best, I guess I have limited sympathy for the idea that the "rolling thunder" should perhaps explicitly be called a thunderclap.
I actually thought 25-WI-K was kind of obvious because you're told Katherine is given the moniker K - it took me longer to find 01-ST-12 because there's no scene in which you're ever explicitly told Rupert is 12!