In this paper we present state of the art coupled-mode space based Non-Equilibrium Green Function approach for modeling quantum transport accurately in the vertically stacked Silicon nanowire (SiNW) FETs. Random discrete dopants (RDD) and metal grain granularity (MGG) induced variability in stacked SiNW FETs are also investigated. Furthermore, charge spectrum, current spectrum w.r.t. sub bands and the space-resolved Local Density of States (LDOS) corresponding to the location of band edge are analyzed in detail. The newly developed flexible and computationally efficient models implemented in quantum transport simulation tool NESS provides valuable insights on the effect of RDD and MGG variability on Sub-Threshold Swing (SS), Threshold Voltage ( \mathrm {V}-{TH}) shift, On/Off Current ( \mathrm {I}-{ON}/ \mathrm {I}-{OFF}) ratio and quantum confined charge transport mechanism. © 2019 IEEE.