Vertical coupling between the lower and middle thermosphere due to the eastward propagating diurnal tide with zonal wave number 3 (DE3) and the 3.5 day ultra-fast Kelvin Wave (UFKW) is investigated using Thermosphere, Ionosphere, Mesosphere, Energetics and Dynamics-Sounding of the Atmosphere using Broadband Emission Radiometry (TIMED-SABER) temperatures near 100 km and Gravity field and steady-state Ocean Circulation Explorer (GOCE) neutral densities and zonal winds near 260 km. The analysis is performed between ±45∘ latitude during 2011, when reliable and continuous measurements are available. With geomagnetic and solar effects removed, DE3 and the UFKW are identified as dominant sources of day-to-day variability at both heights. Evidence is found for the vertical propagation of DE3 and the UFKW from the lower to middle thermosphere over a range of time scales. Over 60% of the variance due to DE3 and the UFKW at 260 km is traceable to variability occurring at 100 km. The not exact agreement is thought to be due to the influences of wave-wave interactions, zonal mean winds, dissipation, and inherent transience that interfere with one-to-one mapping of structures between 100 and 260 km. Spectral and temporal analyses of the SABER and GOCE data also reveal the presence of sidebands due to the modulation of DE3 by the UFKW. These secondary waves are responsible for up to 10% to 20% of the longitudinal and day-to-day variability. Overall, vertical propagating waves together with sidebands from DE3-UFKW nonlinear interactions are responsible for 60% to 80% of the total variability, while geomagnetic and solar effects correlated with ap and F10.7 account for less than 20% of the variance.