I don't know about a spirit in the tunnels because of a well-placed Lovecraft reference in the name of the tunnel.
"Miskatonic".
Warning:Lovecraft Nerdout ahead
In lovecraftian lore, The Miskatonic river fell in the town of Arkham and, more importantly, along side of the town of Dunwich. Those who know the story "The Dunwich Horror", knows that in the town was invisible creature that was the brother of Wilbur Whately, and who's father was The All-in-One and One-in-All, Yog-Sothoth, an Outer God, or cosmic diety.
Now, what if Journal Man was playing the part of Wilbur Whately, and is taking care of whatever is down there? Considering the visible shaken-state of the man, and the journal entry alluding to his explorations, he has to have seen what was in the sub-tunnels, the invisible light, the "body-mod junkie", and the bundles of meat and bone that seem to be writhing around in herds(packs, murders, whatever the hell you want to call it) about the hallways of wherever Dave and Mike are.
All and all, The story builds a fantastic aura of horror lovecraftian themes while it stays it's own entity. Bravo, mr. scott, Bravo.