I use puppy wipes too. I like to keep my boy clean.
Like Megansmomma said, your pup is far to young to be away from his momma. What is done is done I guess, and it's best you learn how to care for an infant pup quick. Conditioner is not only good for the coat, it also conditions the skin, almost like human lotions do for us. Make sure you rinse off all the shampoo and conditioner off your baby, otherwise it will make him itch and it will look like dandruff. A better shampoo is Bio Groom, you can get it at PetSmart, so I'm pretty sure you can get it at PetCo.
For his ears, you will need to see a vet about that. Try to keep his ears from getting wet in the bath. You can give them a quick clean with a damp washcloth after the bath. So far, I've had nothing but compliments on Kaji's ears.
On the food, there is much better food out there than Science Diet. Stay away from anything you can pickup at the grocery store. It's all puppy junk food. Read up on dog food here and check out this website to get an idea on what food is better.
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Also, if you switch his food, do it real slowly. Since he's so young, keep him on whatever his breeder was giving him.
The dragging his bum on the floor can be a sign that either his anal glands need cleaning, or he has worms. Again, check with your vet.