We grossly underestimated the time we needed and missed many sites on our wishlist (including the Scott Monument and Real Mary King's Close -which was sold out!).
Among my favorites that I did see:
The People's Story at Canongate Tolbooth.
Palace of Holyroodhouse and the Queen's Gallery.
Scottish Literary Walking Pub Tour (terrific).
Scottish Parliament building.
Gladstone's Land.
The Museum of Childhood was ok if you are interested in toys and games. The Writers Museum was underwhelming, but at least it was free. I recommend avoiding the John Knox house. Five pounds to get in and not informative or
interesting at all.
We only ate at one great restaurant, The Witchery, and it is definitely NOT inexpensive.