Wendy - of course it's up to you and your DH what to feed Zach. I only keep harping on the milk issue because you've said in the past how much better/less whiny/happier he was off milk and then it seemed like the problems started again with hidden milk (McDonald's fries) and cheese, etc. So between that and what the immunologist said about no dairy until at least 2, I'd be inclined to stick strictly with that myself.
That said, of course any diet is not a magic bullet. Babies/toddler certainly are often high needs and whine, etc. Marsia often does too. And of course she does so less when she's had a good night of sleep, eaten well, is distracted (at gym class, play group, etc) but she still does it some and that's just how they communicate right now. It helps when I work with Marisa on her vocabulary (read books, look at flashcards) and work on challenging skills like stacking, sorting, coloring, etc.
Also, Zach doesn't seem to eat much period - could he be whining because he's hungry? Sometimes a drink or healthy snack helps stop Marisa from whining/fussing.
IMO I'd be REALLY strick about Zach's dairy free diet for at least 2 weeks and see if it helps - at the same time realizing it won't be a cure-all and also focusing on really keeping Zach occupied and teaching him skills to ease his frustration. And like Stacy said, it's also important to focus on yourself, your marriage, etc. Good luck with whatever you decide!