Thanks for the replies! His weight is great and he is super happy. Sleeps wonderfully. No skin issues. He doesn't has mucous. He would occasionally have mucous when he was small and even flecks of blood a few times. He is still nursing a LOT. This undigested thing has really only been happening this bad for about the past month. I know that part of it is that he eats some things that are pretty hard to digest and he does swallow them whole. Things like goji berries, these Go Raw cracker things with sprouted seeds, grapes (cut in quarters, come out in quarters). He used to digest freeze dried mango well, but even that is coming out in chunks.
I don't eat wheat or soy and very little corn. I do eat a lot of raw milk, raw goat cheese, and homemade kefir. When I was pregnant with him I cut out wheat, corn and soy. I only added some corn back in after muscle testing said it was okay for me. When I eat wheat I get leaky boobs and watery milk, so I don't eat it.
I'll supp both of us with some zinc and see if it makes a difference. If not I'll do an elimination diet. I was sure hoping the undigested stuff was "normal" for this age. I don't want him going down the path of gut issues.