So the cow's milk yogurt was a digestive disaster. We quit after three days of giving him - get this - only 1/8 or 1/4 tsp/day. That's IT. I'll spare the gross details, but his diaper had enough evidence to tell me that cow's milk yogurt was NOT agreeing with him.
Goat's milk yogurt next, and yes, it is still homemade. Firmented (aka cooked) for 24 hours to get lots of good bacteria going. That is the whole point of this: get good bacteria in the digestive system, replenishing what he doesn't have, to help with absorption of nutrients from the food he eats.
The first attempts at making yogurt, especially the very first time, were so nerve-racking that I nearly had a nervous breakdown. Heat the milk, but ONLY to 180-185 degrees and if it goes over then you've KILLED it. Oh, by the way, the milk should be raw milk. (That's super easy to find - NOT. We'd need to buy a share of a goat from a farm nearby, and I ain't doin' that until I know it works for him.) Then let the milk, which has not gone above 185 degrees, cool to between 65 & 70. Then add non-dairy yogurt starter, cook at 105-110 degrees (again, don't go above 110 or you'll KILL it) for 24 hours. Yep, 24 hours. Thank God my mother gave me her yogurt maker so I don't have to come up with some twisted way of keeping this fragile stuff at the precise correct temp for that long. Refrigerate for 8 hours. Then (no, we're not done yet) I have to drain the stuff because it's so liquidy. That takes another 8 hours. By the time this process is done, it really is a gorgeous and tasty plain yogurt, but this is nuts.
I'm nuts too, but I'll do anything if it might help him.
We are on our second batch of goat yogurt, and the BMs are getting less and less, well, loose. He's actually starting to eat it on his own now too. Good sign. Stay tuned for continued updates.