Yes you can store your luggage with the GFC in their check-in area and they will also take your luggage to your room for you with no extra charge. Same when you check out they will come to collect your luggage for you, it's much easier than carting it round the hotel!
You can book your meals in advance over the phone or they will do this at check-in for you. I've done both and never had a problem with securing reservations.
The GFC breakfast is in the GFC lounge/breakfast room. I have eaten in the parks in the past for no extra cost at breakfast but this option was not available when I last went. That may have been that they weren't doing it or it may be because GFC get a much quieter and cosier experience than eating in the parks for breakfast.
You get a free pastry buffet in the GFC every day between 4 and 6pm but the pause gourmande is used in the parks and has longer hours to redeem it.
Cafe Mickey is an excellent choice and for breakfast and also offers you a hot option as well as better character interaction ie more characters! There is an extra charge for this but I have always done it. If you have the time go for the first sitting at 8am and you can stay there till they finish serving breakfast at around 10:30pm. This way you can stock up on breakfast to keep you going and you also get to see the character rotation as sometimes they swap characters for the different sittings