I'm not totally clear what the behaviour problems are in this kitty? I guess you mean the apparent boredom and the distrust of other cats?
There's a chance that she's not actually bored, but just being cat-like! Generally cats that are bored will have destructive issues (my cat likes to wreck the toilet paper, for example) If you want to give her some activities, buy a bag of toys and rotate them so she doesn't get tired of them (keep some in a drawer and dole out new ones once in a while). A perch near a window where she can watch the birds might also perk her up! Make sure you give her some quality playtime at least once a day. A toy or feather on a string should get her chasing!
Most cats are solitary animals. Often they will like having another friend or two, but often cats that live in the same family will just ignore or avoid each other. It's not like dogs, where being on their own is an indication of some deeper problem. I think being frightened by the bigger neighbourhood cat has given your little girl a scare, and I can't blame her for not wanting to be around the other cats! Since she is comfortable with her brother, I really wouldn't be worried about big problems in socialization.
If you're concerned that there is a bigger problem at work here, (for example she's not bored, but just has no energy, ever) make sure you take her to the vet!
Great job in handraising a kitten! It's not easy work.