I'm not sure why your ped isn't a fan because we know that cow's milk protein through the mother's milk can give a baby disgestive problems which lead to blood in the stools and mucus.
If you are bf it might also be due to a nipple injury - have you got any cracked or sore nipples at the moment?
It might be that if he really has a cow's milk protein problem the blood in stools is a sign of intestinal bleeding although the bleeding usually happens in the bowel so it would be odd for it to come back out the 'top end'.
Blood in spit-up is more likely to be down to a nipple injury or if it is related to intolerance it might be more about increased spit-up (which is also a sign of dairy protein intolerance (BTW not the same thing as 'lactose' intolerance)) and with the increased spit-up he has broken a tiny blood vessel in his oesophagus.
This is quite a good overview of the issue:
http://www.kellymom.com/babyconcerns/food-sensitivity.
Bottom line - yes, it could be related to the intolerance. However blood in spit-up is one of things you want to get a doctor's opinion on so I would get it checked out when you can. And if you see a lot more blood take him to the hospital to be super safe. Best Wishes.