Hi, we've been to DLP twice, DD is almost 4 now and a Disney pro :)
If you email customer service in advance of going and tell them you need a special pass you will be able to get one which will allow you to wait in special areas (many times at the exit of rides) to avoid the big queues. Or you can just go on the day to the customer services building which is on the left hand side once you get into the main Disney park just before you get to Main Street. If you do this perhaps bring a copy of your DLA statement or a letter from your son's doctor but to be honest no one asked us for this but best to be covered just in case.
You should also email and let them know you will need a ground floor because of your childs needs, that shouldn't be a problem at all but best to let them know in advance.
We stayed at the Santa Fe the first time we went, the rooms are very comfortable but breakfast was manic. It's a huge restaurant and to be honest it felt a bit like a scrum. But its free so fill up! I'd go either as early as possible and get to the park just as it opens or have a quick snack in your room, go do the parks for a couple of hours and then come back for a late breakfast and a rest before hitting the parks again.
The buffet restaurant at the Santa Fe is outrageously expensive and not very good, I wouldnt' recommend it at all. You'd be better off eating in the Village where the best restaurants are. Cafe Mickey has the character meals and you don't have to order anything outrageously expensive either. You and your son could share a pizza (they are quite big) and a dessert and spend under 20 euros and get to see 5 or 6 characters too.
Breakfast at Cafe Mickey is wonderful and relaxed and the characters spend lots of time with you as its less busy than other meal times but its a set price buffet and since you're getting free breakfast at the hotel would mean its a bit of an expense but we did it the second time and we glad we did.
The one thing that bothered our daughter at the parks was Main Street, the piped music was a bit loud and it seemed to confuse her a bit but once we got past main street she was fine and loved it! She even loved rides like Pirates of the Caribbean and the Haunted House (which she thought was funny) and of course its a small world :)
I would say just in case, as you're taking an expensive pushchair, that make sure your travel insurance covers the chair as I have known someone have their chair stolen/mistakenly taken and they weren't covered by their insurance so when we went we made sure the travel insurance covered our pushchair.
I'm a bit of a Disney nut so feel free to PM me if you have any more questions :) Hope you have a great time!!!