It is not uncommon for a pup with parvo to take several days to actually make a stool. Usually the problem starts with completely liquid diarrhea, and the intestines are basically empty. Once they are able to start holding food down, we start by only feeding small amounts. It isn't unusual for it to be 2-3 days after starting food before an actual stool is formed. I even see this in adult dogs recovering from diarrhea from whatever cause.
Yes, it is possible for pups with parvo to develop intestinal issues, but what we see in those cases is delayed recovery, or recurrence of vomiting after they seem to be doing well, and loss of appetite. If your pup is continuing to eat, and isn't vomiting, and is gaining energy back, then I would keep plugging along. A BM shouldn't be too far off. If he ever starts vomiting or looses his appetite, you should recheck with your vet asap.
Let me know if you have more questions.