but please consider that the pet store may not be wanting you to replace the puppy. they would lose whatever profit they may have made from the sale of your new one. and so the vet they have hired would do what's necessary to keep your li'l loved one alive until the contract expires on his health. do they offer a year guarantee on genetic issues? when did you purchase your pup? i know that i'm being somewhat cynical here but i hope they're looking out for your pup's best interest and not their bottom line, as so many do.
found this link about vaccination induced anemia you should read through. i don't recall it saying anything about dark stools....but i'm certainly not an expert.
http://www.gcvs.com/internists/imha.htm
he might be anemic since he's losing some blood through his stool? perhaps he got into something that perforated his insides a bit?
as for liver shunt, i've heard that vets can run a bile acid test to check for that but that it's not a guaranteed diagnostic tool.
i sincerely hope that all goes well for you and your fiance as you help your tiny loved one through this difficult time.
be well