Scot. Your wife is a gem and the 2 of you communicate better than you realize. I can see it from what I've experienced in life with my miscommunications. Mine never got resolved and several Mulligans were in order! You guys resolve yours even if it takes a Mulligan.
You are very hard on yourself when you are being a great dad. Your wife did the right thing by leaving and you did the right thing by continuing to enjoy time with your son. It just worked out that way. Autism and the reactions to stimulation are unpredictable and you are learning continuously to buffer your son from the stuff that doesn't work. That's what a good dad does.