calypso - I've had a few go-rounds with aphtous ulcers. They usually respond well to a mouthwash called "Magic mouthwash". Your Doc/Dentist would actually have to write out how much of what ingredients they want in it because it can contain any number of different medications. The first 2 times I had equal parts of Milk of Magnesia, Tetracycline, Dexamethasone and Lidocaine. After that we dropped the antibiotic.
The Milk of magnia helps to coat the mucous membranes and keep the medication on them. Tetracycline is a basic antibiotic. Dexamethasone is a steroid and Lidocaine relieves the pain.
I used this 4 times a day. Before each meal and before bed. This relieved hte pain so I could eat and fall asleep.
I'm glad that whatever is happening to you is resolving after the antibiotics and hope it's all healed soon.