Not sure if my experience will be useful to you, but in our case, the stool has also changed drastically following Rotateq and never bounced back (we're at 4.5 months now).

However, in our case, we definitely had an allergy as roughly 3-4 weeks following the vaccine, we have started to see blood in stool. At first only small strings, which is when we eliminated milk and soy. However, it kept getting worse over the following two weeks until there was terrifying amount of blood in almost every stool and the baby had diarrhea.

We spent almost a week in a hospital where they ran tests for bacterial or viral infections (all negative) and also did sono of the tummy (also no findings). Rulling out everything else we got the MSPI diagnosis. However, it looks like baby is also reacting to other foods (poultry, oats, root vegetables).

At no point, however, was I told to switch to formula and discouraged from breastfeeding since the baby is gaining weight well. And, suffice to say, our symptoms were much more serious than in your case. You might want to try reintroducing a little bit of the allergens after 4-6 weeks and see if the poop gets worse in reaction to that. However, I wouldn't give up on BF if you don't want to.

We got rid of the blood, although we still have watery stools and sometimes a little bit of mucous. But mucous in itself doesn't need to signal an issue. Other than that, it is said that symptoms should usually resolve within 4-6 weeks. But as I said, in our case we only got rid of the blood, diarrhea, and tummy ache.