The study of the power density spectrum (PDS) of fluctuations in the X-ray flux from active galactic nuclei (AGN) complements spectral studies in giving us a view into the processes operating in accreting compact objects. An important line of investigation is the comparison of the PDS from AGN with those from galactic black hole binaries; a related area of focus is the scaling relation between time scales for the variability and the black hole mass. The PDS of AGN is traditionally modeled using segments of power laws joined together at so-called break frequencies; associations of the break time scales, i.e., the inverses of the break frequencies, with time scales of physical processes thought to operate in these sources are then sought. I analyze the Method of Light Curve Simulations that is commonly used to characterize the PDS in AGN with a view to making the method as sensitive as possible to the shape of the PDS. I identify several weaknesses in the current implementation of the method and propose alternatives that can substitute for some of the key steps in the method. I focus on the complications introduced by uneven sampling in the light curve, the development of a fit statistic that is better matched to the distributions of power in the PDS, and the statistical evaluation of the fit between the observed data and the model for the PDS. Using archival data on one AGN, NGC 3516, I validate my changes against previously reported results. I also report new results on the PDS in NGC 4945, a Seyfert 2 galaxy with a well-determined black hole mass. This source provides an o Show Partial Abstract