FishNHunt--Obviously there are no provable answers to your questions, but I will venture forth with some theories.
First of all, there's no doubt specks were once found in the Smokies at much lower elevations than is the case today. There are plenty of examples of that fact in print. In the pre-logging years (most logging took place in the period 1900-1930) they were plentiful far downstream from where found today.
As for getting above falls, natural transplantation could come in forms such as a kingfisher or hero dropping a live fish above a natural barrier, eggs getting moved by birds, or in some cases, bad flooding offering a way to get above a waterfall. Of course, if you go back to the period when all the glacial activity connected with the Laurentian Shield reached far to the south, you have lots of other forces in action.