I agree with much of your scenario, although I do think that the most likely reason the mound builders were so depleted by the 1700s was due to disease brought from Europe. It is estimated to have wiped out up to 90 percent of the pre-Columbian population. As for the relative size of the nomadic hunter gatherers, I have read that they were not as large, and resided much further south, prior to the Spanish. After they got horses, they rode north for the buffalo hunts, ate a lot more meat, got more populous, and grew in average size and population. I have no doubt there was lots of internecine warfare as well. They were not angels, although some tribes were more warlike than others.
internecine warfare = survival of the fittest
A result of war is absorption. The weak are absorbed away