I just read a post from one of my rando pals on an email forum where he said (among other things) :
"I always seem to have some period of adjustment in the early season when my body (including GI tract) seems to need to get used to the physical stress of events. (I've got a ton of cold sores right now.)"
At the end of the Great Divide Race last year my friend Trish complained of mouth sores as well. I'm not a doctor and I don't play one on the internet but back in 1999, before I rode Paris-Brest-Paris, I read almost everything I could find about distance riding and the strains it puts on the body. And one article I read (it was on paper and no, I don't have a reference handy) was written by doctor who'd ridden PBP and developed the serious cold sores that kept him from eating. He theorized that the sustained effort and sweat would lead to a leaching of the B and C vitamins from the body. B and C vitamins are water-soluble and you really can't store a bunch of them in your system. But you can take daily B and C supplements.
I'm not a big fan of drugs (coffee excepted, I'm a huge fan of coffee!) and I pretty much don't even take things like ibuprophen. But I do take a daily "Stress-B" vitamin, which is a B & C vitamin mix. One brand-name is "StressTabs" but you can read labels and find generic equivalents. Since I've been taking these, I haven't had any problems with mouth sores on the longer events. One side-effect you should be aware of is that excess B-vitamins will be flushed out in your urine, making it a bright yellow. Don't worry about this, the bright yellow doesn't mean you are dehydrated, just that you've got more than enough B in your system.
Keep 'em rolling,