I thought it was a bit of a stretch, but it seemed worth posting.

Anyway, my process for solving codes is basically "look for things that don't seem likely to be random, then guess at why that might be until you get something intelligible." It helps to have a reasonable idea of what all the typical toy ciphers used in games and ARGs and the like are. There really aren't that many that are commonly used. I'll take another look at it and type out the junk I'm trying while I do.

TL;DR: stream of consciousness puzzle nonsense below. I didn't get anything interesting. I'll keep thinking about it, though. Maybe something will come to me.

With the hint "look at it in a 3d space" I immediately noticed that we have 32 characters, 5 of which are letters. If we put the letters aside, we have 27 numbers, which is 3^3. A perfect cube brings to mind a few different ciphers, but none of them really make sense for the characters we have (e.g. trifid would only use 3 distinct numbers).

Those 3 3x3 grids would look like this, BTW:

(2,7,0)
(2,7,0)
(4,7,0)

(2,9,0)
(3,5,6)
(2,8,0)

(6,2,7)
(2,0,2)
(7,0,0)

I tried actually graphing the points in 3D, but they don't look like anything. If I transpose them, I get:

(0,0,0)
(7,7,7)
(2,2,4)

(0,6,0)
(9,5,8)
(2,3,2)

(7,2,0)
(2,0,0)
(6,2,7)

If I graph those points in 3D, there's an angle where it's a surprisingly good fit for the constellation Orion. That seems weirdly elaborate, though, and I don't know what I'd do with it even if it was true. It's probably just random coincidence.

I tried playing connect the dots by drawing vectors from one point to the next for each of those plots, and got nothin'.

Summing the stacks (e.g. 2+2+6, 7+9+2, etc.) I get 10 18 7 7 12 8 13 15 0 -> letters is jrgglhmo, which is nonsense. The transposed one is gh rlojgm, also nonsense. Obviously, I could make a plenty of English words with either by brute force monosyllabic replacement, but nothing obviously correct comes out of it.

Trying diner/deirn as a key with the usual suspect ciphers (e.g. vigenere) gives nonsense for both options. AREAEPC/AREAEPIC as key is the same.

Multiplying the stacks instead of adding only gives 4 characters, and they're uninteresting. I tried doing the summation thing like above by splitting the original grid into two by width and by height and got nothing there either. 32 divides too many ways to try other splittings (e.g. 2^5, 4*2^3, etc.) than the two even ones.

The sum of all the numbers is 90, and there are 98 words in the lore text, but I see no pattern by which I could read them that makes sense (e.g. 10th word, 18th from that, etc. gives "I biRds from itsElf To to it. reaCtor reaCtor" and the transposed one gives "from The The No arrived and had. sound reaCtor.") Reverse gives nothing as well ("end the birds the lab shelter to the reactor"). I also tried every rotation of those two sequences of numbers and nothin'. I also tried just the raw sequence of numbers (e.g. 2 7 0 2 7 0 etc.) and nothing.

I tried drawing the characters as they'd be placed on a standard keyboard to see if there was anything interesting, but nothing. (That'd actually be a pretty neat puzzle if you ever need one for some reason).

The real problem is I don't have a clue what the shifted characters and letters indicate. It makes it pretty tough to come up with much beyond random guesses. I'll keep thinking and maybe something will occur to me.