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The focus on the character numbering system makes it sound like it has to follow specific rules. (Namely the order people die in.) But the numbers are really just the agent's shorthand for the different voices he's transcribing. It could have been anything. In fact I think it would have been better to have them in random order since the system isn't really death order because Hobbes dies after Katherine and he's not part of the chain. So I don't think using 13 instead of "K" would be "highly confusing".
As for Rupert (01-ST-12) being harder to find; I guess that's another example of people having different views on difficulty. It was stated in 00-audio-recovery that there were "twelve victims found in and around the house" so I think it's clear that there should be a number 12 death somewhere (edit: the audio-recovery file was found at 01-ST-12, so it can't be a clue) and with the only unaccounted thunderclap being in timeslot 01, it's just a matter of finding what room it could have been in. I found it easier to find just because it did follow the normal scene code naming convention where persons have numbers. So it was logical that the number would be 12 (or possibly 0). It would have been MUCH harder if had been named 01-ST-R or something.
btw, another confusing clue I was reminded of now was the statement in 00-audio-recovery: "they were only able to recover about a minute from the thirteenth body" which refers to someone as number 13. Another suggestion that there should be a person with that number.