The highly flexible HALE (High Altitude Long Endurance) aircraft analysis methodology is of interest because early studies indicated that HALE aircraft might have different vibration and aeroelastic characteristics from those of conventional aircraft. Recently the computer code Nonlinear Aeroelastic Trim And Stability of HALE Aircraft (NATASHA) was developed and used to the flight dynamics and aeroelastic analysis of flying wing HALE aircraft. Further analysis improvements were required to extend its capability to the ground vibration test (GVT) environment and to both GVT and aeroelastic behavior of HALE aircraft with other configurations. First, the geometrically exact fully intrinsic beam theory was extended to treat other aircraft configurations modeled as an assembly of beam elements. It includes auxiliary elevator input in the horizontal tail and fuselage aerodynamics. Second, the methodology was extended to treat the GVT environment to provide modal characteristics for model validation. A newly developed bungee formulation is coupled to the intrinsic beam formulation for the GVT modeling. After the coupling procedures, the whole formulation cannot be fully intrinsic because the geometric constraint by bungee cords makes the system statically indeterminant. Third, because many HALE aircraft are propeller driven, the methodology was extended to include an engine/nacelle/propeller system using a two-degree-of-freedom model. This step was undertaken to predict a dynamic instability called ``whirl flutter," which can be exhibited in such HALE aircrafts. For simplicity, two fundamental assumptions are made: constant approximation on the propeller aerodynamics and the use of equivalent three-bladed counterpart for two-bladed propeller system to obviate the need for Floquet theory. The validity of these assumptions is verified by investigating the periodic effect of side forces and hub moments and the periodic inertia effect. Finally, parametric studies show how the current methodology can be utilized as a unified preliminary analysis tool for the vibration and aeroelastic analysis of highly flexible HALE aircraft.