Hi, ds,
I'm assuming that your lodging will be within the city limits.
Unless you are hooked on Rabbies' tours, there are several other tour companies in Aberdeen which are just as good, if not better.
The Maritime Museum and Provost Skene's House are conveniently located in center city. Fittie is actually walking distance from center city. It would be about a 20 minute walk at a good pace from the Castlegate.
The best centrally located pubs are the Prince of Wales and Ma Cameron's. Both pubs serve excellent food, so that would fulfill both your pub and restaurant requirements. Also good is Old Blackfriars in the Castlegate (They have deep fried Mars Bars, a Scottish delicacy, as pudding (dessert)!). Archie Cameron's is another good choice, although it's now part of a chain. You won't run out of places to eat in Aberdeen, but avoid the "spit and sawdust" pubs, such as the late, lamented Peep Peep's.
And speaking of deep fried Mars Bars, no visit to Stonehaven would be complete without a visit to the Carron Fish Bar, where said delicacy was invented.
A couple of things that you could do on day three would be a visit to Duthie Park, and its amazing Winter Garden, or a walking tour of Old Aberdeen and King's College. The Art Museum is also good (and free!).
Hope that helps.
Best wishes,
Mike (Auchterless)