Leaving food down all the time is a big no no. He should be eating when the food is offered and that's it. You should call the shots at meal time, not him.
I am not a fan of feeding puppies from bowls but if you insist, I would put the bowl down and if he doesn't start eating immediately or stops mid way through, take the bowl away! Black and White. If he was a mature adult I would say don't offer again until the next meal time but since he's a growing puppy I would try again in a few hours. This is a crucial time and you want to imprint your puppy right. Leaving food down all the time is allowing him to manipulate you. Would you let your child leave their partially eaten breakfast on the table to nibble at all day long? I doubt it so why is it ok to allow a dog to get away with that? They should eat what and when is offered or go hungry. If you allow them to "pick" all day you can create a finicky eater which there are many threads on this board about. This topic is a real pet peeve of mine.
I would ditch the milk bones for now, and reward with his kibble. Subtract what kibble you use for rewards in training from his daily meal ration. I prefer feeding ALL my puppies food from my hand through training but realize not everyone is willing to do this.
ps how much kibble are you putting down per day?