We have read up so much about introduning a kitten to resident cats and are doing everything we feel is right, but it's not working. I know it's only been 48 hours but it's so upsetting to see our 2 resident cats having a go at each other and of course it's so upsetting knowing the poor wee kitten cannot get out into his new house yet as the other 2 are seemingly no where near accepting it.
Welcome! I've been through a similar stuation recently with my new cat and my friend, a neighbour cat. They used to be friends, but when I reintroduced my cat, they didn't seem to see eye to eye. I felt very upset and helpless for the first week or so. But gradually they started to accept each other again; there are random hissing and growling and sometimes even short attacks, but that's part of the "fun". So my first advice to you is give it time and don't dispair.
Missy is a more independent nature. She is frustrated with the change introduced (the small kitten) and redirects her anger and frustration on her more docile sister. In other cases the redirected anger materialises in scratches all over the owner's hands.
Another aspect: Missy needs to make sure she reinforces her right to territory. Being an independent cat she has a broader territory and she cares about it. Normally she can tolerate her quiet, submissive sister, but with the kitten around (from whom she doesn't know what to expect yet) she is nervous and her sister is a nuisance to her as well.
What might happen next: in worst case scenario, Missy will become increasingy upset and eventually reject everyone, turning into an aloof cat. If the kitten is a fighter and he stands his ground, especially after he gets bigger, he might chase her off or bully her. He might accept her sister better, since she is hardly a threat, being so shy. Remember he will need a territory of his own too (you might consider it as a wider personal space.
Another possibility is Missy forming an alliance with the kitten to bully her sister. Finally, the two sisters can team up and bully the kitten and if he is a shy nature he might forever seek shelter in his room, which is not a very nice thing for his morale.
There is a slight possibility for everybody to accept everybody, but this will take a lot of time, so you need to be prepared for what's coming: hissing, growling, occassional fights, chasing, hide and chase games, in one word: trouble.
What you can do: don't allow the kitten in with the girls for a while. When you finally do, don't pet him in front of them. Pet both the girls when they are together and also when they stay separately. Don't force them to eat rom the same plate, put 3 litter boxes, 1 for each cat and at least 3 plates for the food. I recommend feeding the kitten separately for a while (Missy might think he is a threat to her food.
If the situation improves, it's jolly good, however you need to consider the possibility they will never get along and you might be forced at some point to relocate one of the cats.
Question: is the boy spayed?