Here is an article I found on vaccines and inflammatory bowel disease connection:
https://www.dogsnaturallymagazine.co...sease-in-dogs/
There are others that I read years ago when we first stopped vaccinating my dog, but I can't find them right now.
I do know that I, myself, started having food intolerance after I started getting yearly flu shots. I can't eat anything with egg in it anymore.
My holistic vet wrote a vaccine waiver for our county dog shelter so that she didn't have to get rabies vaccine anymore. They didn't have any problem with it. Also, we lived near a lake which means lots of wildlife. I was always very nervous about taking her for a walk near there, but we did okay. I hated giving up the bordatella since she was always susceptible to coughing and in hindsight, it is the one that we should have kept up even though she didn't show, didn't go to the groomer, dog day care or boarding. we always lived in apartments around other dogs.
In the end, the one thing that seemed to make the biggest difference in stool quality was the elimination of flea treatment. I stopped that as a last resort and because we had moved to an apartment with an artificial grass dog run where all the dogs are supposed to do their business (gross.) I still think my precious baby (RIP) caught a dog virus from in the dog run. I couldn't find a vet that would prescribe her anything but heart medicine after the xray results and I think she could have done much better with a prescription cough suppressant. Anyway, she is in a better place now and free from pain. I love her and miss her dearly.
Best of luck with your picky eater. Please have the liver and pancreas enzymes checked regularly, maybe keep an eye on the heart periodically too, if the vet will allow that. They can't always detect anything going wrong with the heart thru the stethoscope until it's almost too late.