Try opening up a cap of probiotics at dabbing the canker sore with that. I know doctors who suggest that for chemo patients with good results. B Complex high-potency. And also take the probiotics for your poor gut. The bacteria balance will be upset after your bug and it can take a while to get a good ecological balance after something like this. Besides caps, there are probiotic foods: Raw Saerkraut, raw kim chee, kombucha tea, yogurt and kefir if you tolerate dairy. Have several servings a day but start with small amounts to see how your gut feels.
Glutamine also helps the mucosal lining of the gut to heal faster.
Make soothing smoothies in a blender with flax seeds and water with cinnamon/vanilla/stevia to taste. Flax has lots of mucilagenous goo in it that will coat the gut lining. Also lignans and fiber that the good bacteria thrive in.
As your gut heals your mouth will heal.
Avoid sugar like the plague!