Aw, 9 weeks old, they're really just babies.
Sounds to me like Dora is smelling their mom on them and it's making her protective of her space. If you think about it it makes sense. They're babies, they smell like the litter they came from and their mom. The mom just gave birth 9 weeks ago so she has a very specific scent and it can make other females (even fixed females) aggressive and territorial.
Poor little Dora, I just want to hug her. I think that she'd proabably get along great with Kilala, sounds like they both have attitude. :)
It sounds like you've got it all under control. Let Dora be around them (without contact) as much as possible. Sniffing distance, nose touching, getting used to eachothers scent.
I would wait until the babies are fixed before really bonding them with Dora, but play it by ear.
If Dora calms down, doesn't lunge at them or show aggression you can start having a few play sessions. One at a time, not both babies and Dora, otherwise bad things can happen.
Eventually, once they're individually bonded with Dora, you can place all of them together.
Make sure that Vaughn is with you when all three bunnies are together, you'll need the extra hands just in case you have to break up a fight.
Can't wait for more pictures. :)

