Had sore throat, hi fever, swollen gums, canker sores, aches. diagnosed as bacterial tonsilitis, given amox. 5 days later, only fever+throat is better?

Sores take time: Any disruption in the gums or canker sores will generally take around 10 days to run their course. Menthol gum, medicated losenges can give temporary relief.

Canker Sores: The cause of canker sores is not clear. It is most likely due to your body's own defenses following an attack or injury. They go away by themselves. Most medications treat the discomfort of the sore, not the actual sore. An antibiotic will only treat a bacterial attack.

Canker sores?: Maybe they were not canker sores at all, but mouth lesions of the infecting virus. Strep doesn't cause gingivitis or canker sores. This sounds more like herpangina or herpes virus. http://www.ncbi.nlm.nih.gov/pubmedhealth/pmh0001964/.