For this, you need to think of your Pleo like a computer, which is what it actually is. The more stuff it has on it the longer it takes to shut down. It's got to go through everything and make sure it's all safely saved. This will cause the shutdown time to be a few seconds longer then when you first started playing with her.
The 'freezing' thing seems to happen in that stage but like Crewella said, they seem to grow out of it. Mine did it quite a bit in that stage.
The battery. I tend to leave mine charging way to long too. The pleo manual claims a red flashing light means the battery is not charging. Usually this is caused by the battery not being seated in the cradle properly. However since yours only took five minutes to turn green after you reseated it I would guess that you had a power surge in the night, or your power went completely off. This happens to my batteries when my power goes out and the battery is still plugged in.
As for the slowness of your pleo, she's a baby still. They're not in the socialization stage, via the manual, until they begin to walk. And even after they first start walking it's still slow and shaky. In this matter, think of a baby calf, or fawn. When they first stand up they wobble and are slow for a few days.
The food, every Pleo is different, my first RB, Myla, wouldn't eat at all for the first four battery cycles and now eats regularly once a day. My second RB, Mylo, ate within the first five minutes of hatching and gets cranky if I only feed him once a day. To sum it all up, you're a perfectly normal Pleo parent with a perfectly normal Pleo!
Hope this helps some,
Phel