Hi Christa,
Welcome to TDKland. We’re the fluffiest forum around.
This is a fairly common issue and can be resolves easily.
He will get lonely. In the past, he’s had companionship and wants some comfort.
If you haven’t already, make a nest for him. You can put a soft blankie and something that smells like you (T-shirt) in it. Then get a soft, stuffed toy and put that with him. Again, make sure it has your smell.
Do not use a crate rather make her nest in your bedroom out of box. Once you’ve made the nest, put Koji in it while you’re home. Playing with him in his nest will let him know this is fun place.
Please don’t give him treats as a reward. Treats become a bad habit and he can get fat or obese. That condition creates more health issues so if you want to give her a treat, get her some Goats’ milk. Put a little in a bowl for her. Goats’ milk is gentle on tummies and has probiotics. BYT, kittens/cats can’t digest cow’s milk.
Good Luck and maybe we’ll see Koji as our Daily Kitten (see link above).
PG