Can't really give any
advice re your dog or vet, but one thing I have observed in one of my dogs is that if I feed too rich a food (ie high protein and oils/fats) her ears get very irritated and red and very waxy :( - just like an infection, but it goes away when she's given less rich/ simpler food
I do think a serious ear infection could cause temp, sore neck and lack of enthusiasm for food tho ;) - although it's possible the injection also caused a sore neck ;)
Have you been back to your vet to discuss this?