I agree with lv4dogs. Obedience training is a must! I was disappointed to read this:
I haven't been doing the nilf, because she is well behaved.
NILIF is a series of very simple tasks. It's not like a 6-week obedience program. It's very simple and very doable. For example, you say she woke you up on your bed. I'm going to assume that she's allowed to sleep with you. Don't let her do this anymore. A crate will be a better option. As well, you say she'll hold out on her kibble until your daughter feeds her tidbits. Don't allow your daughter to do this!! Runner will *always* hold out on her kibble because she knows that your daughter will eventually feed her yummier foods. Instead, feed Runner in a different room or different time and ask her to "Sit" before each meal. There, NILIF is initiated!

I'm going to take a leap of faith and guess that you treat Runner pretty much the same way you treated Charlie. If so, are there any things you can modify to create desirable behavior? For example, you say that both Charlie and Runner are beginning to eat their feces. While the exact cause is not known, most people believe that dogs eat their feces because their diet is deficient of certain nutrients. My dog, Lucky, also used to eat feces when he was a puppy. He was on so-so food that contained lots of corn and by-products. After several food switches, we found a kibble that completely agreed with him. He does not even touch poo anymore.

My point: Change Runner's food and see what happens.

I wish you the best of luck!