I dont put vitamins in her water. Should I? I've thought about it. She isn't puffed all day. just when she is napping and relaxing.
NOOOOO! Don't EVER put anything like vitamins or other supplements, or any type of medication like Antibiotics in her drinking water, and if any Vet ever tells you to medicate her drinking water, then you need a new vet. First of all, you have no way of knowing how much of whatever you're putting in the water your bird is getting, which is dangerous, and secondly it contaminates their drinking water immediately, growing all kinds of bacteria, fungi, etc. Only give your bird medications by exact dosage/amount either right into their beak with an oral syringe, or by putting the exact, measure amount into a little bit of food. That's it...
She should get all of the vitamins/minerals and nutrition in-general that she needs from her daily diet. Only if a bird is diagnosed with a nutritional deficiency or metabolic issue by an Avian Vet should they be given extra vitamins/minerals, and that would be by injection...
****As far as your Quaker being sick,
how is she doing since the beak grinding/toenail trim incident? That would be my major concern, as you said she wasn't acting normally days after that happened to her...If it weren't for that incident and her behavior after it for days I wouldn't worry, but based on just that and the fact that she's still not acting quite right, if I were you, I would find the closest Certified Avian Vet or Avian Specialist other than the one who did that to her beak/toenails, as they are obviously not going to be objective and just tell you there is nothing wrong with what they did and send you home...You need an objective opinion, as it's quite possible that she was injured during that experience, or that she inhaled enough of the beak dust to cause an infection in her lungs/UR system, as they had to wash her off she was so coated in it...
At this point I would not feel good about letting this go any longer, not because she "fluffs-up" when she's sleeping, that's normal, but because she seems to be sleeping too often and is actually what I would classify as "lethargic" based on what you've described...