With regard to preserving the stratigraphy, I would try talking with
     Colonial Williamsburg.  I know they had some similar things on display
     some years ago.  I am not clear if what they depicted was the actual
     stratigraphy or if it was reconstructed, but they have been
     interpreting archaeological sites to the public for many years and
     probably can advise you.  The folks at St. Mary's City and Jamestown
     should have some useful suggestions, as well.
 
     It sounds like a wonderful site.
 
     Liz Crowell
 
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