Is the outside wall sitting on a foundation or just built on top of a patio deck. If you have a foundation, you would build the floor and stand new walls to match the house,6" high floor over concrete may be a problem. I wouldn't do anything without footings and foundation. You may want to take the old patio out.
If you are leaving the wall between the rooms in place your local truss company could build add on trusses and they would tell you what and how much of your old roof would have to be removed. The chimney will have to made higher.