You need to be on the balls of your feet more. My kids had the same feeling you are experiencing, yz. Just realise that the balls of your feet are futher forward than what you may first think. Practice being conscience of your foot positioning. It will come.
Danman is telling you correct, you probably want to move your levers. If your brake is too high, you may find yourself riding it when you arent wanting to. Also, try lifting your left foot off the peg when shifting...lifting up with your whole leg to shift up, and lifting it off and stabbing down to downshift. Takes some getting used to. I've been riding for years and I still have the urge to "sit-n-shift".