Okay the vet called me a few days ago. I've just been so busy (I'm a teacher and this is the first week of school in my district!!) that I forgot to post about it.
Those lumps in her stomach and liver were abscesses from infection. She had no trace of the protozoa (either giardia or cochlosoma) left in her system, but she had a terrible fungal infection throughout her entire body.

At least it wasn't avian pox. He said it was probably the combination of the 3 things: being picked on, protozoa, and the fungal infection which was why she just couldn't get better. It was a downward spiral. Once her immune system was down from being stressed, she was unable to fight off the protozoa, and once that took hold, she couldn't fight off the fungal infection, and then the other birds picked on her because she seemed weak, which stressed her out and lowered her immune system response further, and so on.
OH! Also, Owlie was apparently a BOY! I was shocked, because he never sang, the other owls would sing to him, built a nest for him, fought over him, and even mated with him lol The vet said he was just acting very submissive because he wasn't feeling well so the other birds treated him like a girl. Also, the breeder put a pink leg band on him. Come on. What was I supposed to think?
Well, anyway, hope that info helps someone in the future. Thanks again for all the support and kind words. I am probably not going to be very active in the next few days, or even weeks, the beginning of the school year is always so crazy!!!