You did not give the dates of the population estimates in your initial post, thus I assumed they were from a later period. Also, the first epidemics entered the continent from the Gulf Coast in the mid 1500's, I do not find it unbelievable that the epidemics killed a large percentage in the St. Laurence valley before 1600. The initial Pilgrim colony at Plymouth was established on the ruins of a village that had been decimated by chicken pox (?) and abandoned.
Fairly sophisticated if you ask me.
The only major change was that there was more extensive exploitation of marginal crop land (marginal for corn-squash-beans) by grazing meat animals upon the land. If you want to convince me that Jefferson's agriculture was massively more productive than Cahokian, show that the addition of draft animals increases farm production (excess for sale off of the farm) by at least ten fold.