http://scpsandbox2.wikidot.com/moenennbys SCPs ; The Jordain Estates, Maeneclay Manifesto
This feels a little bit all over the place at the moment. You have exploration logs, book excerpts, personal letters, mysterious houses, advanced alien civilisations, an interview and some multiverse stuff. That is laudably ambitious, but for me it never cohered into a single story - I never felt as though each new angle was developing my understanding of what came before.
That may be because (I must admit) I started skimming by the time I got to the Letters to Emma. There had been nothing that sucked me in, so I went looking for "the good stuff", but I didn't really find an ending either. Full disclosure, I'm not completely sold on the Academy idea, so this skip would need to convince me of that idea, rather than it working the other way around.
In terms of improvements, I would start by laying out the story you're planning to tell, and the order in which you're planning to tell it. Make sure that each piece of the story leads clearly on to the next, and that the order of telling draws the reader further in all the time (eg by increasing scope, or deepening characters, or challenging assumptions).
I would lose the opening warning, as I never got the sense that the main document had been written earlier than the rest. And the Description needs to be made much more specific (ideally with less blackboxing, although I assume you're choosing that deliberately) - "SCP-XXXX is a large structure built on an island" gives the reader very little to chew on. Especially when it turns out that it's not always a large structure, or on an island?
And if you keep the exploration logs, you should change them to add more character - whether that is slowing down the descriptions to focus on reactions, or including dialogue - at the moment the team members are interchangeable and generic, so the action loses immediacy.
Lots of other stuff to suggest, but I think it's best to overhaul this structurally before looking at the drafting.