Sounds like you are doing fine with the home first aid on all the sore spots. The clavamox should help the healing on the other areas too.
Yes normally nose pigment comes back once the area heals.
And yes you are absolutely right that dogs can get kennel cough after being vaccinated for it. Its a viral infection and the vaccine only covers a few of the common strains. The antibiotics she is on should keep her from going into bacteiral pneumonia which can be a secondary infection that goes with the viral kennel cough.
If the sores on the face and feet spread this could be puppy strangles (horrible name but breathing issues are not a symptom of it) an autoimmune problem you can read about here
http://www.lowchensaustralia.com/health/strangles.htm
Hope this helps you!
Dog Expert:Rescue, Train,Breed,Care
30+ yrs dog home vet care & nursing, rescue, behavior&training, responsible show breeding, genetics