Hi Sally,
I love that you are bringing your son at an early age. I am so glad mine started when they were little as the park has changed for us over time and it just proves how ageless the park is.
I would opt for the Magic Your Way ticket and skip the extra options. You want to slow the pace and enjoy your son at the park. When he is older, you can add the options but there is enough to do now at his age. I would plan a character meal as a special treat. I love Crystal Palace with Pooh and friends and it is where my children first got their special hugs.
If your son likes to nap during the day, you may consider staying at a deluxe resort to save time on traveling. It also makes it easier to handle the stroller and other gear by staying off of the Disney buses.
You also want to make your Advance Dining Reservations (ADRs). You should note your son's allergy to milk and they will accommodate his needs at his meals. If you have questions about items at the counter service restaurants, you can ask for the chef to advise you on options. If you feel more confident about bringing snacks from home, you can throw his meals into a small backpack and you will be fine. I will say Disney does a great job with food allergies as my shellfish allergic daughter can eat at the clam bake without an issue.
You can look at the moderate hotels for a room with a free refrigerator, deluxe has them as well, and you can email specialdiets@disneyworld.com as well for any additional questions.
Wishing you a magical vacation!
Beth