I have a clearer image of the cipher in the bunker - I'll double check tonight to see if I can get a better image of the Dragon room piece, but last time I tried it doesn't allow you to move. But I may be able to go into third person to get a better view.
Also, good job @Draz on that transcription! (: It looks really great! I think since we have pairs of numbers [N, M, O] (where these represent numbers) it would be nomenclatures for those pairs. We would still have a lot of ciphertext with this approach.
My other thought is that this and the other scrap is connected... But since (I think) this is the first time we've had two scraps of paper on a map, it's likely they could be separate. I haven't had too much time to work on this, but hopefully I can get to it soon!
Good job to everyone who has found and worked on this! Kudos to you!
EDIT: I went through and added the frequencies of the sequences. This makes me think that these could be words (Based on their freqs) and that the numbers are nomenclatures for letters. This is similar to the cipher in DE, but in this case we do not have a chart to go off of. But, we can perform "letter" (number) frequency on these and distribute accordingly. The catch to this will be that some letters will reoccur more than once, so they will have multiple numbers associated with them. This will be more tedious than difficult I think. I'll start on parsing your text file, @Draz, and seeing how many times each one appears. Since we have so much, we should get a pretty clear frequency graph. Once I figure out how to upload things, I'll add my text file.
EDIT2: I've finished it: Letter Frequencies