Yes, the Polynesian 'Club Level' (Hawaii Longhouse) has third floor connecting rooms....we stayed in rooms #3508 & #3509 a year ago. It was great having our daughter and our grandchildren so close; we left the connecting door open the entire 7 days we were there. FABULOUS views of the lagoon, Cinderella's Castle, the Electric Water Pageant and night fireworks....and a great balcony.
When we checked out, I asked the concierge desk how we might get connecting rooms for a future vacation and this is what he said to do:
1. Initially make two phone calls: first one to the main Disney reservations (phone 407-934-7639) AND the second one to concierge desk in the Hawaii Longhouse (phone 407-824-2000 & ask to be transferred to the concierge desk; concierge desk is open 7am-8pm)--tell them you're traveling with family and request they put "travel with" on your reservation (this is the unique term they use) AND request connecting rooms.
2. Ten days prior to arrival: make those two phone calls again and request connnecting rooms
3. Day before arrival: call the concierge desk in Hawaii Longhouse and again request connecting rooms. The concierge desk makes all the room assignments for guests staying in the Hawaii Longhouse and they usually do this in the afternoon or early evening.
4. Day of arrival: check-in as early as you can at the concierge desk in the Hawaii Longhouse (NOT at the Polynesian front desk). Concierge desk opens at 7am (my husband and I were there at 7am; the night before we stayed at the nearby resort, 'Shades of Green'). If arriving by bus/car, go to the free standing Concierge desk OUTSIDE the Polynesian to left of the main entrance sidewalk--they will take you directly to the Hawaii Longhouse to check-in.
Have a wonderful vacation!!!! One more thing--the concierge lounge has large bottles of Evian water that they allow you to take back to your room...we put them into the room refrigerator and would then refill our plastic water bottles as needed.