If you're looking for a couple places to eat downtown, try Lowcountry Bistro or Poogan's porch. They're more of a "locals" place. Actually, since you're staying in Mt. Pleasant, try out Red's on shem creek.
Yorktown is pretty neat, also the boat ride and history of Fort Sumter, but you can also go see the Hunley in N Charleston. The aquarium is "ok" as far as aquariums are concerned. I dunno if yall are into fire trucks, but there is a fire truck museum next to the Tanger outlets.
It's really hard to sum up Charleston in a few days, but it sounds like you have a good start. If you have any more questions, you can PM me. I've lived just outside of Charleston my whole life.
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