Maybe look at it like a taxi trip. You can fight your way around this whole trip trying to get everyone in one taxi at the same time(or dinghy trip) or you perfect the divide and conquer approach early. Ring up the charter companies with your dates and times. Do not worry about the number or size of the planes let the air taxi services workout the best options with the inventory they will have on those days. With each additional plane you likely get the added bonus of one more "co-pilot" seat to fill. Those seats will be coveted in most groups.

Once AA backed on on the number of flights our standard approach is to get to San Juan the best you can and arrange for one of the air taxi operators to great each arriving part of the crew shortly after they get of the plane. Most of the pilots are great help gathering the luggage and getting it loaded. The family grabs a short potty break and the flight on the small planes is alway exhilarating with incredible views. For the view the smaller the plane the better. Sometimes with Disney getting into the park is half the fun. The same with the last leg by air taxi. Be honest with the weight of all your baggage, dive gear, electronics, coolers with meat.