I just wanted to respond to the part of your post in which you mention your suspicion that your son could fit through a small pet door. You are probably correct. My in-laws have small dogs, and "small dog" doors in their house, and my two-year-old daughter can fit through them with startling ease.
My best suggestion with regard to keeping the food/litter box off-limits to your son but not to your cat is to make a big point of it with your son. We keep our cats' litter box in the downstairs walk-in shower, which is never really used, and their food/water is close by. Any time our daughter has shown interest in these items over the past year or so, I have given her a stern "no touch", similar to what I have issued when she has ventured near the stove. I think if you save your most serious rebukes for just a few really important no-no's, most babies will absorb the message after a few repeats (and lots of vigilance in the meanwhile). I say that even as the mother of a VERY determined, headstrong child.
Good luck keeping both your baby and your kitty companion safe and happy.