I would guess #4 as well.......... it seems the most likely culprit, unless, during all the switching and changing, something on your hands or items may have had contaminants on them.
I think #4 is unlikely and very improbable. I've never subscribed to that theory. If it were true you'd see the tank load gasping at the surface every night. Ammonia spike, some kind of anaerobic built up in the bottom, contaminents seem far more likely.