Okay, I'll address each issue point by point:
Pictures: I agree. It was the best I could find in the SCP Fuel pictures. I may have to keep looking for something better or remove them entirely.
Change in radiation wavelength: This is related to how the wavelength of light increases as it travels away from a gravitational well, causing a red-shift. In those cases, time is slowed closer to the centre of that object. With this anomaly, time is sped up inside, so the radiation blue-shifts rather than red-shifts. I will add some additional information to it in order to make that more clear.
Biology: We're going with gut flora. It's really the only form of life I could think of from which I can get an ecosystem (if there is another source you can think of, I am willing to consider it). As for the time span, the time differential is greater than you might think, especially as you near the centre of the phenomenon. Though I might, as I think about it, increase the number of expeditions that occur before the slime starts appearing.
As for conservation of mass, that's not really an issue. You did point out a hole that I'd forgotten to fill up, though, and I appreciate that. I'd intended to note that there is a large deposit of organic matter within the Black/Green Zone, deposited over a long time by various bacteria slowly falling through the Red Zone and dying. Now, I know what you're thinking! If all these bacteria keep falling in there, why hasn't this ecosystem appeared earlier? Well, while our happy little D-Class passed through the Red Zone quickly, allowing some minuscule percentage of bacteria to survive the transition, the bacteria that would have found their way inside naturally would have either been embedded in or on top of the rock on the cave floor, or wafting down via air currents. In both cases, the bacteria spend too long in a high radiation environment before they reach the safety of the Green Zone. This might be a bit long-winded in the article itself, though. Maybe I can add a supplementary page and call it "The Natural History of the Green Zone".
Wording of the zones' descriptions: Yeah, I hear you. I'll work on it.
Number of digits: I understand your concerns there. I do want it to be large enough to sustain some sort of macroscopic ecosystem, but I'm still able to raise it so that it's closer to the Earth's surface. I'll have to think of some sort of mechanism that causes the cavern to be a lot cooler than the surrounding mantle.
Green/Black Zone distinction: Another hole that I'd forgotten to plug (thank you!). Was meant to note that the title was changed to the Green Zone upon the discovery of the developing ecosystem. It was originally the Black Zone because you couldn't directly see what was inside, due to wave diffraction (a 100 Hz light wave would not let you see much detail, after all).
Mutations: Again, the amount of time that passes within the Green Zone is greater than you might think. I'll make that clearer.
SCP-111: I admit, the zone naming was partly borrowed from that (even if I didn't remember its designation). I hope I won't be accused of plagiarism because of it. If it is too close to the mark for people's tastes, though, I'll look for some other naming standard. Though the rest of the article is pure Flah.
So, you guys have given me some very useful feedback. I wanted to address the points before I started working on revisions. Thanks again, everybody. Hopefully, the revised version (currently pending) will feel more natural.