Whole atmosphere models that fully capture the propagation of wave dynamics from lower to upper atmosphere are believed sufficient to reproduce the type of short-term variability in the neutral upper atmosphere that produces observed variations in ionospheric parameters. However, recent studies suggest that upper atmospheric observations are needed to accurately represent short-term variability in both planetary-scale mass transport and tidal behavior crucial to representing the structure of the thermosphere and the wind-dynamo coupling in the ionosphere. To address this, we use atmospheric specifications from the prototype High-Altitude Navy Global Environmental Model (HA-NAVGEM) from the ground to 92 km to nudge the Whole Atmosphere Community Climate Model extended version (WACCM-X) coupled to the Navy Highly Integrated Thermosphere Ionosphere Demonstration System (Navy-HITIDES) ionospheric model. The HA-NAVGEM data assimilation/forecast system is run in two configurations: a reference experiment for the time period December 2012-March 2013, where satellite-based middle atmospheric observations (SABER temperature retrievals; Aura MLS temperature, ozone, and water vapor retrievals; and SSMIS microwave radiances) are included between 20-90 km; and a perturbed experiment, during the same time period, in which the middle atmospheric observations are removed. The resulting nudged simulations using WACCM-X coupled to Navy-HITIDES are used to study the impact of upper atmospheric observations in reproducing the observed short-term variability in the thermosphere-ionosphere system, both in terms of the thermospheric structure and the ionospheric response via wind-dynamo coupling. The role of solar thermal and lunar gravitational tides is discussed, as well as the impact of observations on the weather of the day in the lower thermosphere.