Does the poor little guy have diarhhea or is he just going poop at odd times? I think you did a good thing taking him off the treats, he may have a sensitive belly to those and need something not so rich. Also with him being so young, the traveling may have messed up his potty schedule a little!
Welcome to you and Kody, I am positive you will get a ton of responses to your question
with a ton of advice!