My dogs have always been vaccinated for Kennel Cough (Bordetella) so I have no personal experience with it. It's a requirement here if the dog is to be boarded anywhere and proof of vaccination is needed before they will accept the dog for boarding or pre-scheduled vet procedures that require overnight or extended stay care.
What I do know is that Bordetella, otherwise known as kennel cough, is caused by a bacterial organism (which is what bordetella is), or can be caused by a virus (Canine adenovirus (hepatitis virus) or the parainfluenza virus), and is spread through the upper respiratory fluids of coughing dogs. (Which I am sure you already knew

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Treatment consists of antibiotics and sometimes a cough suppressant and should run it's course in about 10 days.
My only concern would be dehydration from the runny stool (probably being caused by the medication) if she is being left outside in the heat for any length of time. Can you keep her inside where it's cooler and she has constant access to fresh water at all times? I know you are really worried about her but she's on medication and you are doing all the follow-ups with the vet. I'm sure she is going to recover and be just fine!
You can add a little boiled rice to her diet to firm up the stool. Lots of water is always good when they are on an antibiotic.
You're being a normal worried new mommy and that's, well... normal! I know you are giving her lots and lots of TLC and watching her carefully for any changes in her condition. You're on top of it and doing what you can...
She's going to be fine because you're doing everything to make sure of it.
I know you want her to be all better, like... yesterday! But - it has to run it's course. Keep her well fed and hydrated and just keep loving on her... you're doing great.
