Thank you very much for those! I knew about the Faithful Servant note, but never actually saw it and didn't knew it was in such Industry Global Communication Centre appearance. The Illuminati language....this must be proof the letters are from the Novo Ordus Seclorum. So the sender, IHCOMFSOG, is Illuminati, which makes sense. Next to Group 935, Broken Arrow, the Ascension Group and the Ancient Order of the Keepers I am of the believe they are the only ones mastered teleportation (thanks to Richthofen's contribution and their sources in the other sciencific organizations), and so, possibly timetravel as well (though I am unsure how MTD's are capable of BACKWARDS timetravel). Let's consider they are: In 1975 they send the Kino and Five letters to 1963. Why were they first not aware how the Doctor got to this time and place and in Classified they were? I've looked it up, and a few things changed. You see, it didn't went chronological.
Ulimis Der Riese, 1946 --> via overloaded MTD to Kino, 1963 ("we are unaware") --> via Gersch device in Ascension to Siberia, 2011 ("out of time") --> via MTD to Shangri La. Now it get's weird, as Shangri La, naturally, is a weird map. The timeline says that in 1956, Brock and Gary get stuck and Ultimis arrives to help them. However, Shangri La is the only timeline scrap of the maps that doesn't have the map's name as an indicator above it. What's more, Brock and Gary are stuck in Shangri La in 1956, during the Eclipse, but Ultimis travels back in time during the map. On top of this, MTD's are believed to be uncapable of travelling back in time, even when overloaded, and given the fact Ultimis used an MTD to reach Shangri La (heard in CotD and seen upon spawn in Shang)...I think the 'daytime' Shangri La is actually in 2011, like CotD, while the Eclipse is in 1956.
So in Classified's intro, we see Ultimis timetravelling from Shangri La 1956 to the Pentagon in 1963 (Classified) by accident due to Tank overloading whatever they teleport with with the Babymaker. Since it is 1956, I believe they do so during the Eclipse. So in the Ultimis Saga, the only time they use backwards timetravel is during Shangri La. And apparently, this changed everything: "We are aware of how he reached this place and time". Suddenly, They know. What kind of odd thing is going on? Five happens directly after Classified, Five happens at the same time as Kino. So at approximately the same time, there are two Ultimis in this universe.
Kino is abandoned, the Pentagon is not. I think the letter found in Kino is an older one, at the time the Illuminati didn't understood Richthofen's sudden vanishment in 1946 and appearance in 1963. In the time Ultimis went to 2011 something happened that made the Illuminati understand (possibly the appearance of Primis Richthofen?), and so, when Ultimis arrived back in 1963 again, the letter was changed.
I also have a whole different idea: Illuminati warning Ultimis Richthofen for his Primis version that comes to kill him in the Giant or get his crew at the end of Classified. Wouldn't entirely make sense, though.
I like your clarification of the zombified developer xD. So that is a human error, and no weird canon thing we have to solve as well.