In this article, we investigate an extended version of principal geodesic analysis for the unit sphere S2 and the special orthogonal group SO(3). In contrast to prior work, we address the construction of long-time smooth lifts of possibly non-localized data across branches of the respective logarithm maps. To this end, we pay special attention to certain critical numerical aspects such as singularities and their consequences on the numerical accuracy. Moreover, we apply principal geodesic analysis to investigate the behavior of several mechanical systems that are very rich in dynamics. The examples chosen are computationally modeled by employing a director-based formulation for rigid and flexible mechanical systems. Such a formulation allows to investigate our algorithms in a direct manner while avoiding the introduction of additional sources of error that are unrelated to principal geodesic analysis. Finally, we test our numerical machinery with the examples and, at the same time, we gain deeper insight into their dynamical behavior.