The biggest problem with the 5fingers is the whole separating the toes thing. I go absolutely nuts when i have my socks bunch up between my toes. I have to stop whatever it is I'm doing and fix it. I can't function with things between my toes.
As for running, my biggest problem has been my ankles. Well, that and plantar fasciitis. I'm not sure how much of the PF is caused by my shoes. I've always worn Asics because they have the best arch support for my feet. After reading OP, I've tried running in my Adidas Sambas. If you know them, you know they are flat-soled with absolutely no support. I really haven't noticed much of a difference. And it's hard to tell if they're affecting my ankles because ever since I crashed my bike, the left one hurts all the time anyway.