I hope your kitty is doing fine. The symptoms you describe as "signs of an upper respiratory infection" could well be a virus and not bacterial, meaning, amoxi will do no good. Never diagnose a cat yourself, see a vet or a low-cost clinic (check with your Humane association for advice about where to find one).
Hello and welcome. Bless your heart for rescuing your new kitten. As far as medication goes, it would be remiss of anyone here to give you advice. What appears to be a URI could be a sign of other illnesses. You won't know for sure until she is examined by a Vet.
Best of luck~