Welcome. I'll try and answer your questions, but the first thing is to relax!!
This plan isn't some magical formula of exactly what to eat so there aren't any hard fast rules.
The food itself from Wave 1 and 2 is pretty much the same, with the addition of fruit in Wave 2 as well as I think a bit more grain ( someone correct me if I'm wrong here because I am at work and don't have the book here.)
It really is going to be tough to make yourself fat on veggies, unless of course you cover them with butter, oil and cheese. So eat up. Veggies are very low in calories for the most part so if you find youself hungry, always grab for those veggies.
The purpose of the proportions is to retain ourselves on what a "normal" amount of food is. One problem with not eating all the amount of food at one meal is the possibility of becoming hungry and binging. I would say eat your grain with your breakfast, but there is no law you cannot interchange lunch and breakfast meals.. So you can eat you "lunch" meal at breakfast and your "breakfast meal" at lunch.. so have a veggie omlete for breakfast, add some additional veggies to get the 40% protein and 60% Tier 1 vegetables and then have 75% of the plate with protein (such as scrambled eggs) and 25% with whole grains, such as a slice of whole grain toast at lunch.
Dairy plays a minor role in Sonoma so yes you can have it, but think of is as an accent rather than a primary componant in food.