Itty Bitty Feda knows what a good mother she has. She so sweet. 
Not sure I’m picturing your space right. If there’s room, I’m wondering if one of those dishpan drainer things, the kind that go flat on the counter and slope on one side to drain into the sink, would be good to set in the pee/poop spot? I know they are not good to chew on, but if Cotton’s problem is not jumping into a litter pan there, at least it’s low and flat. Could cover it with hay. Or maybe a regular dish pan with one side cut away.
Wanted to ask you when you think you’ll start doing bonding with the two of them? After she’s spayed/neutered? Can it be started before since he’s already done? I hate to see them start a pattern of fighting when they’re both so cute. She probably would let him be dominent, and would like his company. I wonder how he could be convinced that she is “his” the way he is sure that you are “his” (and jealous because of it.)?
Bedtime games can be a real challenge, especially when they stare at you knowing what you want, and what they want, and it’s not going to happen any time soon. You’re lucky his breaking point is Papaya Tablets. He’s a cunnin’ bun!