First, I would keep in mind that you are probably at the most hormonal, tiring, exhaustive phase of motherhood. Not to minimize any of your problems, but, "this too shall pass".
Next, it does sound behavioral. Not medical, assuming the ruling out of anything medical was fairly recent. How many boxes, how are they situated, what kind of litter, ect. While maybe 1 year ago your cats didn't care what/when/why/how, maybe they do now.
There is a book out that talks about cat's bathroom behaviours. I can't recall the name of it, but, I read it and it was insightful. Maybe you can google for it?
As for Aiden crawling...well, you have dogs, cats, and I presume you wear your shoes in your house? Cat poop is probably the least of his worrys. Not saying it is pleasant, and certainly not desirable, but, I think working up to an artifical deadline (Aiden crawling) is just putting more stress on you. Who knows, maybe he will be like Jonah, and not crawl, just walk?
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