I wouldn’t add bone broth to smoothies — BUT, I wrote a post all about gelatin and homemade jello — it’s very kid approved! My kids all devour the stuff, and the gelatin is going to provide all of those good benefits like a broth would. It’s a really good option for kids who don’t love sipping a cup of broth. you can even add it to smoothies as well if you wanted.
As for a probiotic, I would try and stay away from greek yogurt or other commercial dairy if possible. If you have access to raw cultured dairy that would be great (and I’m jealous), but if not, try a supplement. There are lots and varying opinions on supplements. I haven’t tried one for my children, but have heard the brand “bio-kult” is a good one. My kids get their probiotics through sourdough bread, pickles, and water kefir. They drink a lot of kefir! If your son will take it, I would go for even a milk kefir from the store instead of greek yogurt — it has a lot more probiotics and is easily hidden in a smoothie. Opt for the plain variety and just throw it in with some fruit and whatever else you are blending!

Another tip is to not use anti-bacterial soaps and things on him. That just destroys ALL bacteria — even the good stuff we are trying to cultivate! I think you are doing great, your smoothies sound awesome and you are getting lots of good stuff in him with those — good job! One thing that is very destructive on the gut is gluten – have you tried removing it? I know it’s the hardest thing to take away from kids, but people have great results from that! One of the major reasons I am obsessed with natural yeast baking is that it provides great probiotics and breaks down that gluten so it’s not so harsh and can be easily digested. Just an option!