Okay, finally found the time to look at this.
This is a considerable improvement on the last version of the draft I read. You removed the expunged part at the end, added a pretty satisfying ending, and generally tightened things up. I still think the skip is unnecessarily meandering, but even that's not without its charms - still though, you might want to consider applying at least some of the changes psul suggested to shorten/focus the skip. And while all the various elements do coalesce better now, there's still some room for improvement IMO - I feel the different parts could use more of a connecting thread. As this stands, your starting point (the menhir) and end result (the escaped rabbits) don't feel related enough thematically. One solution might be to be a little more explicit about what is going on, and what the purpose of the anomaly is (the hearth god wanting to create superhumans), so the various elements of the skip don't feel as disconnected.
A note regarding the ending: it's neat, and I like it, especially the note by Madeline Weaver. My only gripe with it is that your somewhat ominous build-up in the test logs (and maybe also the fact that you had originally expunged the ending) made me expect a much scarier and more disturbing ending (à la SCP-466). While I don't dislike that you went for a more lighthearted ending, I would have preferred something darker, given where the skip started (an addiction aspect, uncontrollable hunger, plenty of potential for body horror). And the idea of highly-adaptive lifeforms that most people can't "see" escaping a Site, then infesting other Sites around the world unbeknownst to most Foundation personnel could easily be made unsettling and scary, if said lifeforms weren't rabbits. :P I realize this is probably a matter of personal taste, though, but I wanted to mention it regardless.
Overall, for me, this has gone from a skip with potential but with no ending (in earlier drafts), to something much more finished and satisfying that I quite enjoyed reading. I'm fairly sure this would do well in its current state, but as I said I feel this could be made even better with a little more work.