Thank you so much for you super detailed response. I will do the usual spoilers warning! Spoilers from this point on!
Hilariously, I found Rupert a bit earlier on actually. I didn't mention him in the original comment because it didn't occur to me he would be hard to find. I did in fact use the file with Oswald and Martha talking to help me locate Rupert. Also, I have a 9 page Google doc with every single scene and lengthy notes summarizing each scene. In addition to that, I also created 4 charts, one for each act, in which I filled in every character and their location for each time code. That helped immensely even if it took a lot of time.
Huh. Now I am stumped. I must be missing something else because I recounted the bodies and I came up with 13. 1-11 then Rupert and finally Katherine. A small note that the death of 1 occurred in time code 26 and at the entrance. Are those all the bodies? One of the notes from @ said it was just the 13, but now I am not sure. I just am at a lost as to what I could have missed. I did try to research more on both Eleanor and Amelia but neither sound like they could be the thirteenth body based on their descriptions. Rupert says that Amelia went missing one day but it doesn't sound like she died recently. Eleanor was stated to have died a long time ago by Katherine as well, a fact which Oswald also confirms. The drawings Oswald shows Annie also show three children: Oswald, Elanor and Rupert, who Oswald does not recognize. So yeah. I will try to do a search of 00 notes since I did delete my first game due to my assumption I had a bug. As a result, I did have to go back and try to "refind" some of the 00 files.
If it helps any, these are the two files that have a (1) next to them: 21-LI-1-2-4 and 23-CH-1-2. Again, I really appreciate the response as I can at least stop obsessing over trying to find anybody at 00.