Dented batteries and too hot to hold and shorted atomizers make me REALLY nervous. I would hit reset and start from square one......take it completely apart and examine everything; clean and check everything, and do Zoranth's list. Screwing up with li-ion batteries can be dangerous and I believe we lull ourselves into thinking otherwise. All it takes is one incidence and someone can be badly hurt.
Yup, a couple years ago when I was into remote control toys, the lithium batts I used had to be charged in a blast container. It takes about two seconds to find a vid of these discharging on youtube. I doubt these are as bad today, but looking at a battery pack that thinks it's a jet engine might make people think twice. At least with these you don't have to wire them yourself and monitor heat and discharge rate. But you still need to respect the batteries.