Forgot... If your bottle is floating around and is not kept under water, then there won't be any water flow going through the holes if the holes are too small and for a cory that size you can't make them bigger. The box needs to be clipped in at least 2/3 into the water so the laws of physics make that happen.
2-3 water inches water height shouldn't be a problem. Mine is just about covering a big moss ball.
The Ph difference may have shocked them though as you say. A 0.2-0.4 difference for a cory fry is huge shock I would imagine. That's why some type of box providing constant flow from the main tank would be best as long as the tank is cycled and healthy of course. All this "dirty" looking stuff on moss balls, java moss and plants could be mini creatures for them to snack on. I've read and was advised here about adding mulm from established filter for them the first week as it provides great micro-natural food. So super cleanining is not the solution exactly, only if there's some very visible bits of food floating around.