As I referenced above, there is serious designation bloat here. SCP-XXXX-1 doesn't need a designation, as he's not actually anomalous on his own, and neither do these manifestation events, as they are just extensions of the properties of SCP-XXXX-2 instances.
SCP-XXXX-1 accepts this all far too quickly and is far too pliable to be believable to me. Incorporeal versions of himself show up and he's taking lessons from them almost immediately. He doesn't have to completely freak out, but the way he reacts right now is written such that it feels like it's skipping the "wtf" bit of his character arc in an effort to speed the plot along. It's contrived and it hurts his character arc as a whole, which weakens the article quite a bit given it's written around that arc.
The general build-up here isn't bad, but it didn't really evoke any emotion in me. We join SCP-XXXX-1 at the tail end of the events and actions that spark the whole narrative, and by virtue of that, we have very little reason to actually be invested in him as a character and in his struggle in particular. The point of the narrative is he's a person who needs to self-improve, but I never cared whether he did because what he needs to improve about himself is so nebulous and ill-defined that it's very difficult to invest in. Additionally, the way he talks about his own issues is so vague and yet matter-of-fact that it feels like it's barely an issue. The incident that gets him caught by the Foundation, wherein he goes to get a drink and is discovered, only actually felt like a mistake and issue on his part posthumously when the other characters said it was outright because the way he talks about it in the diary entry makes it sound so utterly normal. It's a dude going to get a drink, and unless you've really explicitly set up and cemented the fact that that is a problem, readers won't notice.
The payoff on the build-up here is the biggest issue. The ending just does not work. SCP-XXXX-1 arguing with the SCP-XXXX-2 instances is, broadly speaking, good stuff, but it's hampered by not being well built-up to. One day he's a little tired with the lessons, the next he's completely done with them, and then he's done with the -2 instances entirely. It's all far too fast and jumpy and doesn't feel natural. Additionally, the reasons for his response aren't well communicated. It's all told to the reader; vaguely through the diary entries, and then more directly in conversation with the -2 instances, but it's all telling and very little showing. Why are these lessons so bad? Why are these books so bad? Why are these exercises so bad? You need to show the reader this, rather than telling them rather vaguely. That's what separates really quality writing from the standard stuff.
The final issue I'd like to raise is the ending.
Addendum: After the conclusion of the events recorded in Surveillance Log #3, the maximum time between occurrences of SCP-XXXX-A events has increased to 8 days.
Perhaps this is just me, but I don't know what this is meant to indicate, metaphorically or literally. Does it mean the -2 instances are just visiting him less often because they're annoyed with him? Or are they not giving him lessons anymore? Or…? It's unclear, and it causes the ending to lose any impact it might have had. On top of that, this doesn't work as a strong payoff. If the idea here is that the -2 instances aren't actually helping him, then the payoff should reflect that more clearly, because right now all that's happening is it's telling us they've fallen out. It's not impactful, and it's far too flat. It's a too-neat ending that doesn't feel like it actually says anything, so it doesn't feel satisfying.
This isn't a terrible draft, and there's a solid framework here, but the current execution and presentation of the story don't work for me. It's not focused enough on the important elements of it's own story, and by virtue of that, it's unsatisfying. It's not unworkable, and with some revisions, I could see myself more on board with this article. Good luck!