Thank you, everyone, for your responses.
I thought about the pumpkin but we don't have any on hand, so I'll be making a trip to the store today. (I just realised this morning that I haven't left the house/garden since the puppies arrived on Saturday - except for the vet trip.)
As for the vaccinations, it's something that we discussed with the breeder. She isn't a fan of over-vaccination, but these are the ones that she thought were prudent. The timing of the vaccinations was probably influenced by the breeder not wanting to let them leave without getting their first shots. Our vet also recommended bordetella, which we will discuss with the breeder, as they will be exposed to other dogs when they start puppy kindergarten.
The wormer was Strongid-T and our vet commented on what that didn't cover - which is the reason we want the fecal test.
The food they are currently eating (which I won't name because if anything is more controversial than vaccinations, it's dog food [

]) is a commercial dry puppy food (chicken and rice based) that is commonly used by many reputable breeders of Shelties in our region. Over the long term, I plan to slowly transition them to a home-prepared diet. However, I won't start that until they are at least 9 weeks old.
So, my plan is:
* call the vet about dropping off a stool sample earlier than planned, just as a precaution
* slightly reduce food intake for the larger puppy (she has been getting a little more than her brother because she is close to 4 lb and he is only about 3 lb)
* add a little bit of pumpkin to their food