There's two criticisms I have, one a lot bigger than the other. I know, I know, criticisms again.

But you've still got me hooked without a clue as to what's going on, because despite everything screaming 'man-made disease', stuff just does
not add up, like sentient stoves and winged moons.
But back to the criticisms. Firstly, the size of the Bloodletter was never mentioned. Initially, I was envisioning it about the size of an octopus (not a giant octopus, a normal one). About the size of a beach ball. Especially when you used the word 'head' to describe it; that gave it some implied size. But it's obviously way bigger than that. While that became more obvious as the chapter went on, it initially threw me.
But the second criticism is I think what did the most damage, and it's not even anything to do with the writing. It's just this: I needed a map. I definitely got the sense of being in a maze, because I had no
idea where Thomas was or where he was going. When you mentioned specific places, I had zero context to visualize it. This really cut down on any tension I think, because I was constantly trying to reconcile what you were describing with an image in my head which just didn't exist.
This was most obvious when Thomas was at the A checkpoint. Part of this was a lack of description on the room itself, but not all. At first I thought the Bloodletter was behind him, talking through some window. But then he was blocking the way, so he's... ahead of him, but can't get in. But then he leaves... what? Why is he leaving? There were references to some other long way around... I got really confused reading that whole bit.
There's two ways I know of to deal with this. One is obviously to include a map. Mapping an interior is pretty fast in photoshop, and really comes in handy for things like this. A second method would be, if you know keeping a map in the head is going to be difficult, don't try and explain where on the map people are. Instead of referencing specific points and specific routes being taken, just say Thomas knew the way, and continued down it. When he comes to checkpoint A, describe the room as somewhere he knows he needs to pass through, but don't bother describing it in relation to anything else. This method would leave the reader more able to focus on just the tension and action, rather than trying to track progress.
Now, all that being said, take it with a grain of salt, because I have been known to get lost in small nature parks, grocery stores, and parking lots.