I will definitely do research on everything you listed. Thanks!
I found the email we received from a local before we went. It was three years ago so take it for what it's worth. Good luck!
Restaurants:
Slightly North of Broad - East Bay Street - our favorite. Casual but very nice. Chef's table gives good view of kitchen which is fun to watch. Professional locals eat here at lunch.
High Cotton - across street from SNOB - a little more formal, live music at the bar usually at night.
Magnolia's - next to High Cotton - similar to HC
Bessinger's Barbeque - Highway 17 South - very good pork barbeque and onion rings
Peninsula Grill - never been there but heard it is very good, and very expensive
Husk - avoid as it is currently very trendy and what they cook is a bit strange
Southend Brewery and Smokehouse - micro brewery is good, food so-so.
Avoid Fleet Landing, Bubba Gump's, and most other places alongside the Market as they are very touristy. Most places require reservations for dinner and some recommend them for lunch.
Museums:
Nathaniel Russell House - Meeting Street, the best house museum in downtown. Nice garden. Clean bathroom above gift shop at back of house.
Edmonston-Alston House - beautiful also, down on the Battery.
Heyward Washington House - Church Street, beautiful furniture but house itself not that much to look at compared to above two.
Middleton Place - Highway 61 west of the Ashley, beautiful gardens, nice house similar to Heyward Washington inside. The garden party scene in The Patriot was filmed there.
Drayton Hall - Highway 61 also, beautiful preserved empty house, no furniture, so-so gardens.
Avoid Boone Plantation and Magnolia Gardens as they are tourist traps. Avoid Calhoun Mansion, very tacky. Avoid Charleston Museum - looks like it contains what the locals cleaned out of their attics. Avoid the Old Exchange & Provost Dungeon - not much to see there compared to the others.
Other:
South Carolina Aquarium - very nice, takes about 2 hours to see.
St. Michaels, St. Philips, Cathedral of St. John the Baptist - mostly open to the public during the day but no organized tours as far as I know.
The Citadel - parade most Friday afternoons about 3 PM.
Ft. Moultrie - Sullivan's Island, nice to see
Patriot's Point - Mt. Pleasant, Yorktown aircraft carrier, Destroyer Lahey, submarine, etc., nice military museum
White Point Gardens - at tip of Battery, bandstand
City Pier - at end of Vendue Range, fountains, tree lined alley
City Market - tourist stuff but nice to walk through just once
Visitor's Center - Meeting Street, good starting point
Walking tours - lots of different ones available, ones done by Historic Charleston Foundation probably better than most
Tour of Homes and Gardens - never have done one but hear they are nice, done by HCF, gets you into private homes that are not normally open to the public