Second Model
Here I took both the layers and put them together to better show the relationship between the two. Here I cut out around the current buildings to fit in the old baseball field. Also the tall apartment buildings are now protruding through the "old" layer.
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First Pass of Model
In this iteration I chose to make to layers one representing the current conditions of the site (lower layer) and the other is the site in 1905 (upper layer)
The clear areas show the open space, the blue is the water and shore lines.