One illustrative method disclosed includes, among other things, forming a vertically oriented semiconductor structure above a doped well region defined in a semiconductor substrate, the semiconductor structure comprising a lower source/drain region and an upper source/drain region, wherein the lower source/drain region physically contacts the upper surface of the substrate, forming a counter-doped isolation region in the substrate, forming a metal silicide region in the substrate above the counter-doped isolation region, wherein the metal silicide region is in physical contact with the lower source/drain region, and forming a lower source/drain contact structure that is conductively coupled to the metal silicide region.