I don't think there's any particular move you're making that's totally wrong. Hand feeding or putting your hand in the bowl is great for teaching tolerance around the food bowl.

I hate to be mean, but I do think dogs pick up on personalities and with all the questions you've had, you seem very insecure. Not that this is unusual for a first time owner, especially if they've been exposed to extreme training methods like the dog whisperer. I don't believe you have a dominant personality to begin with. Dominance does not mean you are mean to the dog or some sort of punisher. It means you are confident and can lead naturally. Know what you want to do and do it, don't go into a situation with anxiety that it may not work. Its not really something that can be taught though, only developed perhaps with time and experience.

On another note, I think sleeping in the pen is a bunch of bologna. Yes, it great for a dog to be comfortable in the pen in case of emergency, but it does not make you any more of a leader. Let a puppy sleep on your lap and they will learn to be secure and totally relaxed around you. Make them sleep in a pen and they will be a "lone wolf" only secure enough to be sleeping deeply when they are alone, alert and awake when you let them out to be around you. Why would they have to be alert and awake when they are around you if they can trust you? Don't forget to play and have fun and don't worry that tug o war is going to make her aggressive. The bond you form with your dog will determine how well they will listen to you. Free-will following is always better than a dog who follows against their will.