Jon,
Guilty as charged :)
Steve,
Yes, there are small openings where it was cut that allow some air exchange. Also, as it begins to grow, I plan to slowly unscrew the top to allow some more air exchange as well. Mine barely fit in the 2L bottle. I cut the bottle pretty close to the bottom, giving me a tall top section and a short base. I place the cutting cup in the base and put a little bit of water in the base to provide some additional moisture (it's in the "feet" of the base so the cup is not sitting in water). Then I loosely fit the top over it. I also check it once every day or so to make sure there is condensation in the cup so it airs out then as well.