It is best to take a puppy inbetween that is not shy and not over active/ bully to be on the safer side.
Good vets generally have the instrument for scanning and getting to know the micro chip number etc. I would not advise on getting the shots put twice.
Generally its the father of the pups that is nice and a champion but the female is quite shitty....... so insist on seeing the pups with the mother, as sometime you will be shown another female and they would say its the mother.
I would advise you to download the puppy registeration form from the KCI website and accordingly proceed for registeration. On this form the owners of both dogs need to sign and attach documents which in turn are sent to the KCI office. What is the breeder saying has he sent the papers for registration. You can also tell him that you will pay say 70% right now and the bal when he gives you the papers.
Before getting the pup home please read on the net about getting a new pup home etc. As you need to puppy proof the home, get bowls for it, toys, bedding, brush, etc. Food is also very important and ask the breeder what they are feeding the pup, try and feed the pup that food for a while before changing it to another if you want. There are various manufactured foods available depending on the dog breed and age, like Roayl Canin, Eukanoba etc. You will also have to give your dog calcium and multi vitamins as per the vets advise.
So dont be in a hurry and first prepare yourself and then pick up the pup, the puppy should also have a puupy pen where he can play around without getting into trouble and also where you can put him for little while. Do not tie the pup he is too small. You will need to start basic training also slowly. The list just goes on so do the homework and all will be fine. All The Best. Please also read about the first night of the pup as he will be very unhappy and will howl the entire night it can be for a couple of days also, as he will miss his family etc.