Spoilers
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You can't use 00-audio-recovery as a hint to find 01-ST-12, because that file is found inside 01-ST-12.
Personally, I think the numbering system being the way it is was a good call. On a meta level, if the numbers were random then the player would at one point have to be directly told a number for Rupert, which would have been extremely conspicuous since he's a non-speaking character. It's also logical in the story that the agent numbers things in a consistent order (at least, before he realised the K thing) rather than assigning them randomly. And as other comments say, if the number system stays, K has to stay, unless you're willing to number her 1.5.
I kind of agree on the thunderclap - to me, rolling thunder isn't quite the same as a thunderclap. Personally, I would've liked a bit more of a hint to Wintercote specifically, e.g if Victoria had said "We'll drive to Wintercote, it's only 10km away" and then scene 25 said "thunder can be heard about 10km away". Distant could mean absolutely anywhere, and the only real clue to Katherine is the phone call.