Ferret bullying dog

Question
I have a ferret Kiwi that was wild (in the sense of untouched by humans)until I got her (at an estimated 6-7 months old).
It took me a week or two to teach her to stop biting people she knows, and she still occasionally nips other people to this day.

A couple months after, my roommate got a puppy. We were scared the puppy would try to eat/play and accidentally hurt but the puppy was always nice. HOWEVER it is Kiwi my ferret who was bullying the dog. She started by biting her once on the nose very hard, and ever since the dog is scared.
Example: Kiwi would stare and hiss at her until she gave her bone, Kiwi would steal it and run away with it.

Fastfoward a few months: we worked a lot on the two of them, and the puppy now a dog is OK with Kiwi.
BUT I got a puppy myself, this time a german shepherd which although was a puppy was very dominant. From the very beginning I made it clear that Kiwi is dominant over the GSD. It worked after 2 weeks.

But Kiwi is trying again to bully, just it's my dog this time.
I would try to do what I did when the problem was with my roommate's dog: scruff Kiwi when she starts bullying, but my GSD recognizes the punishment and barking with me and seems to then try to affirm itself over Kiwi.
So I don't yell/scruff Kiwi in front of my GSD, to keep their statuses. My GSD understands she must respect Kiwi, but she is not scared at all of Kiwi like my roommate's dog, and I am afraid this "respect/submissivity" is fragile.

What should I do? :)

I tried to put the information I thought was relevant, but I can answer any questions needed.

Thank you

Answer
Knowing dogs and ferrets, this is probably a case where the two should never be allowed to play together.  GSD's have a high prey drive and a ferret looks and acts a lot like a prey animal.  The noise and fast moving actions will probably always trigger the dog's instinct to chase and pounce.  FYI, no such thing as a Dominant or submissive dog or ferret.  Your ferret would be better served with another ferret playmate.