I mainly haven't replied because I'm not really sure what to say
It seems like they've done pretty much whatever I'd think of. The only time I've had this happen the 2 cats never did end up getting along. It was just a case of they absolutely hated each other, and neither one was the main instigator.
As far as scruffing, I do agree that it's probably not a good idea. When a cat that doesn't take kindly to this is scruffed by the neck they will stiffen up and can get out of your hand and maul you. Scruffing will calm SOME animals down but not all, it really depends on the personality and how they've been raised and handled. Also, I've seen many people that aren't experienced with cats get mauled trying to grab them by the back of the neck.
Heck, even if you're nearby to a catfight you can get mauled. I've had this happen when 2 cats were in a really heated fight before. They slash at anything and aggression can also be misplaced to anything nearby, so I wouldn't suggest getting close to them while they're in that state anyway.