Yes most of those are in the City - Dynamic earth is down by Holyrood Palace and the Scottish parliament buildings. It's 10 minutes into the City Centre, if you are doing a few things then a day pass on the bus might be worth it as there will be a fair bit of walking and it's hilly.
I'd skip the Castle, do one day zoo, one day down to Dynamic earth and go and look at the Palace and if it's nice, take a walk up Arthurs seat, go by the pond and feed the swans and get some views of the City.
If you can manage to change the dates then I'd do a day at the SCience festival.
Otherwise, A trip to the Museum on Chambers street, walk up to see Greyfriars bobby, on to Camera Obscura for the afternoon or vice versa.
You could go down to ship and take a trip along the coast in either direction to Cramond or Portobello for some sea air.
And other day, doing a bus tour, wandering up the high street and Princes street gardens, there is a play park at the west end and the Flower Clock at the junction with The Mound. maybe a trip into jenners toy hall if they still have it or up to Harvey Niks for the Chocolate café for a treat.
There are Theatres and cinemas too if you want stuff for the evening? Loads of independent Italian restaurants for dinner or visit Jimmy Chungs Chinese buffet near Waverly Station for a quick meal.