Welcome to TCS!
It's wonderful that you're committed to keeping all the cats! Sounds like you gave lots of time for introductions, which is great too!
One important aspect once the introductions are over is our own response to conflicts between the cats. It's awesome that most of your cats get along so well but like you said, it's very special for cat that aren't littermates. It would be fine if Chewy and Scooter won't ever become best buddies. The goal should be not to have them put each other in danger and not necessarily much more.
Sometimes, cats fight. It's actually normal in a multi-cat household where cats need to establish their hierarchy. What we often see is that cats fight during the initial phase after introductions and once everyone is content with the new order, they relax. Then, sometimes following an illness or some major event in their household, they start fighting again, as the "lower-ranked" cat tries to undermine the order and establish a new hierarchy (not always successfully).
The thing to remember is that we have zero influence on these things. Just why and how do cats establish their social hierarchy has to do with subtle physical cues, including scent and behavior, that we can't even tell. It is up to them entirely and we need to allow them to go through the process. Obviously, without getting to the point of them hurting each other (which can at times happen - more on that in a bit).
When humans intervene during cat skirmishes it's a recipe for trouble. Here's what happens -
1. Cats sense each other's presence and prepare for conflict. Their bodies put the "fight or flee" mechanisms into action. Adrenaline is rushing through their veins.
2. They begin their calculated dance of threats, hissing, yowling, possibly batting each other.
3. Human steps in. The cats are so focused on one another, they have no clue that a human is even around them. They suddenly hear a lot of noise (human shouting), and sometimes feel something is sprayed on them - a direct physical attack! It's all associated with the object of their attention: the other cat.
Yes, they may freak out and run away, and you have achieved "breaking up the fight", but the price is they now view the other cat as a vile creature, one that can bring on the wrath of the loud noises and water sprays! Definitely foe and not friend!
This is an association you need to break now, to allow them to form a new positive association with one another. It's going to take time and sounds like they have a great owner with a lot of patience to help them through that
How do we do that?
2. Reduce competition over resources. Read more about that here -
3. Work with both Scooter and Chewy on general stress reduction. Here's a few suggestions -
4. Work on positive associations. Give lots of praise and treats when they are in the same room and not fighting. Have a small bag of treats in your pocket and throw them each a treat, making sure they never have to compete over the treats. It's best if they are at the opposite sides of the room with enough distance between them.
5. When they have a negative interaction (hissing or aggressive body posture) even if they engage in a an actual fight - never ever shout at them, create louds noises around, spray them with water or any other form of semi-violent deterrence.
6. Never use your own hands to separate fighting cats. You will get scratched and bit and it can be very bad. If a you have to, separate the cats using a barrier that will break their line of sight. Gently place a chair or some other piece of furniture you can move around easily and without making a lot of noise. Try to drape the chair beforehand so that it creates a barrier preventing them from seeing each other. Once that's in place, very gently use a broom or a similar long stick to move one of the cats into a nearby room where you can shut the door and give the cats time to calm down.
7. Again, patience. It's going to take some time but eventually they should begin to tolerate each other's presence. If they're already content with eating next to one another, you're doing well and it's highly unlikely that they will break each other's necks if they do get in a fight.
Let us know how it's going!