You might want to consider weaning him off all the antibiotics for two weeks and just give the probiotics a chance to work by themselves, especially since he seems to be doing better. I'd probably back off the milk thistle and aloe too since what the right dose size is for supplements isn't always that easy to calculate.
Not only will that give you an opportunity to evaluate him independent of the meds, but it also reduces the opportunity for any bacteria to develop increased resistance to antibiotics. Perhaps just stick to one medication what you think is working best and/or damaging him the least if you feel he still needs treatment.
Mom eating dirt shouldn't be a problem. A goose's digestive system can deal with dirt, even if she seems to be eating lots of it. It's usually because she finds dirt that is mineral rich or otherwise tasty. Unless the soil is contaminated it's not dangerous even if it seems weird.