Mike et al,
Please forgive my delayed response to your query about the guns on the CSS Pee Dee. Just got back home from a few days in the hospital.
The three guns were all fitted as deck pivots with the 7" Brooke (S-46) up front, the 9" Dahlgren (Ft. Pitt #513) in center, and the 6.4" Brooke (S-53) as the aft Pivot. There were also two 24lb bronze howitzers. These had been captured by Wirt Adams from a yankee gunboat on the Yazoo River. Location of the howitzers is unknown, but still tantalizing.