I have a interesting purple second toe most of the time. It's not my longest toe, and my shoes fit fine - not hitting the end of the toe box. But I know that my toes have a tendancy to grip the sole of whatever shoes I'm in, and I believe it is that action in conjunction with running that causes the trauma to that toe.
It's something that I've done for years without being aware of it. I've got narrow heels and I think I do this to prevent shoes slipping off the heels. Didn't realise it until I bought some sandals, and could actually see them doing it!
Not sure what to suggest, but it might be worth trying some padding on or around that toe. I've been trying to spend part of my easy runs concentrating on what my toes are doing when running, to see if I can't train my feet out of their bad habit.