When she was re-engined the old funnel was reused by adding an additional piece to the middle and reusing the outside pieces. I would recommend that you basically do the same with the model funnel.
You definately need a good reference book to follow through her history of changes of which there are many around at the moment. Try the Carol Thatcher one or the Ronald Warwick one, both of which have some very usefull photo's. Main areas, as you say are the aft deck, funnel and the penthouses but there are also changes to the original foc's'le crane arrangement, which went from two to a single crane, and the lifeboats were changed a couple of times since the model period.