Just to throw in my two cents: back in late January when we put Josie on a REALLY restrictive diet -
http://www.bodyecologydiet.com - for a couple months, I discovered it was easiest to cook my own foods from scratch. It was a HUGE time commitment at first, but in a month or so I got the knack of making enough and preparing far enough ahead of time that it got easier. It involved soaking grains and seeds (and eventually legumes when we put them back in the diet), and it drove us nuts for a while - I felt like I was spending my WHOLE TIME in the kitchen - but eventually we were able to put in some "normal" food (which for us was yogurt LOL) and also depend on leftovers once I actually cooked enough.
Cooking meat and vegetables, especially green ones, took the most adjusting to for us. At our grocery, frozen veggies (the easiest for me for convenience) come in 1-pound packs, and we were eating one of those at EACH MEAL for a while - but at the same time we didn't get sick AT ALL for nearly SIX MONTHS. Once I worked out that I had to cook MORE THAN a pound for a meal to have leftovers, we were golden.
The neat thing, though, was that I was eating salads almost EVERY DAY, the girls were eating vegetables EVERY DAY, we were exploring different seasonings, and Josie (who is admittedly older than your LO) became very into cooking - she and DH especially would cook lots of things together, and even now that we can even have pizza once in a while I make sure to include her in dinner at least every other day. The whole family was in better shape, Josie's whole demeanor changed for the better, and oh, yeah, I lost a LOT of weight - I went from about 150 pounds to 125-ish, where I still am now.
I also knew what was in EVERYTHING that came from our kitchen. I knew that there was NOTHING that should cause a problem - that was before I knew about Josie and corn, BTW (turns out that corn makes her act crazy, so she's probably allergic to it
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) - and I felt SO GOOD about making it!
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We all learned a LOT about nutrition and we still have what some folks would consider some pretty out-of-the-mainstream food choices here. We discovered that you can make kefir out of young coconut juice, for example - a nice fizzy drink that Natalie LOVES that is FULL of probiotics! We have also moved on to another food program called Nourishing Traditions and learned lots of cool stuff about alternative (these days) ways to make food - traditional foodways that have fallen by the wayside.
OK, I'm getting pretty tired now and have another 2 boards yet to peruse, so have to go, but wanted to put in another bit. It CAN be hard to avoid soy, but I think that at Whole Foods they have pamphlets for different diets, like dairy-free, gluten-free, and so on, and you can probably get some guidance there. Best thing, though, for us was to just cook from scratch.