There is no 00 scene. The 00 files never have the scene-place-character structure, they're usually information or messages directly from the agent. It is (probably) not an 00 file you missed, they're all explicitly signposted in other files and you could just double check you didn't skip over one by using "find 00".
There are 97 files in total, so you are missing 2.
To help more: every character appears once in every scene in which they are alive. For example, if you check the titles of the 04- files, you should find all the numbers 1 to 11 there. You explicitly meet almost all the characters very early on, being Persons 1 to 11.
This rule alone should be nearly enough to help you work out every file you are missing except two of them. One of the files it can't find, 25-WI-K, you already found, so I think one of the files you've missed is an ordinary file you can probably find by the process of elimination of just checking you can find every living person in every scene. Is anyone unaccounted for at any time frame?
The other file that rule can't find requires a little bit of inference from you. Here's some gentle clues which get progressively more pushing:
1. What signifies the death of a character?
2. Are there any of these signals you've found which don't seem to correspond with a death?
3. When did Rupert die?
4. Where did Rupert die?
5. What is the pattern that associates characters with number codes?
=====ACTUAL ANSWER=====
01-ST-12 is easily missed. It's the only file in which Rupert appears alive. The thunderclap for this happens very early on, in 01-QU-1-11, probably the first file you read. Note that in 01-QU-1-11, Harry Thornton knows who Rupert is for the first half of the scene ("worked for him all my life"), which means Rupert isn't dead yet. The thunderclap then happens halfway through, and Harry Thornton then says Mr Galley... now meaning Edmund.
You also get a clue in 01-LI-3-5, where Oswald and Martha are talking about Rupert in the first half of the scene, saying he just left, until midway through the scene there's the thunderclap.
You'll almost certainly have worked out that character numbers correspond to the order in which they die. Since Harry Thornton is 11, Rupert must be 12. You also know he died in the Study, again from very early on.