I often get mouth sores when my Crohn's is flaring. They can be on my tongue, gums, roof of my mouth, throat, etc. Yes, they are painful and they can linger on for a while. I am struggling with a flare of them right now as a matter of fact. Unfortunately, I haven't found anything that helps treat them with the exception of trying to treat the inflammation of your disease. When I get a flare of them I do my best to avoid inflammatory foods and eat things I know are healing for my body.
They are a result of the inflammation in your body so it's difficult to treat them without addressing the root cause. For me, following a Paleo style diet has helped reduce the frequency of mouth sores, but I do still get them when my Crohn's is flaring.
They are miserable and I totally understand what you're going through.