Here is a first draft of the track plan for the overall layout.
The plan includes a wye at the left end of Aquia Landing. Unfortunately, there is no way to fit a wye without having to extend the tracks through the wall into the workshop. So instead, I'll probably install a turntable there instead.
The pier is close to the front edge of the benchwork to allow access for operations. The deep scene behind will be filled with ship models. This gets them out of the way, and perhaps opens up the opportunity to do some forced perspective modeling using 1/64th instead of 1/48th scale ships.
The car floats will have to be scratch built, as will the side wheel steamer. I should be able to find kits for the tugs and sailing vessels.
To achieve the required height for the Potomac Creek Trestle, the tracks will climb at 2 percent grade as they depart Aquia Landing. Unfortunately, this will not gain enough elevation so the bridge will not be high enough. But through application of a reality distortion field, the water level of Potomac Creek will to be dropped about 5 inches below the level of the Potomac River. I hope that this doesn't create an incongruous scene as the trestle is just on the other side of aisle from the harbor.
This plan shows a stick trestle, but I have still not decided what type of bridge to use there.