I would check the book "Cultivating History: Exploring Horticultural Practices of the Southern Gardner" which is the proceedings from the 2001 Restoring Southern Gardens and Landscapes conference. Several good papers presented at the conference addressed some of these issues. It will of course give you a good list of people to contact since many of the presenters have done considerable research in this area.

Here is a link that might be useful: SGHS publication

Volunteering at a historic site, I've learned a little. Imported stuff had to survive a long ocean voyage under sail, which resulted in a low survival rate for both plants and resident pests. The rate of introduced diseases and insects going both ways across the pond increased drastically with the introduction of the steam engine in the 1800's, and has continued to speed up with every "improvement" in import efficiency (container ships being terrariums). Colonials did import huge amounts of herbs and weed seeds that jumped the garden fence and naturalized across the countryside - like plantain, ground ivy, jimsonweed, etc. They considered much of the naturalizing to be an improvement of nature, since all this stuff was useful to them. However, my colonial volunteer site would have lacked: starlings, chestnut blight, dutch elm disease, anthracnose, botrytis, ladybugs, japanese beetles, red lily beetles, english sparrows, gypsy moths, (possibly) earthworms, etc. But introduced by that time would have been: pigeons (brought in by the French), the honey bee, hessian fly, norway rat and many plants we now categorize as noxious weeds. Most of the accounts that I've read from the time period note that American soil was more fertile than European, and European crops lacked some of the diseases of home. For example, Josselyn (1672) describes peas grown in N. America as "the best in the world" and adds that "I never heard of, nor did see in eight Years time, one Worm eaten Pea." Books that might contain some info: "Early American Gardens" and "Eighteenth Century American Gardens" by Ann Leighton, "Indian New England Before the Mayflower" by Howard Russell, and "New-Englands Rarities Discovered" by John Josselyn (available in reprint from Applewood Books, Bedford, MA).