Gravitational microlensing is a powerful tool for probing the inner structure of strongly lensed quasars and for constraining parameters of the stellar mass function of lens galaxies. This is achieved by analysing microlensing light curves between the multiple images of strongly lensed quasars and accounting for the effects of three main variable components: (1) the continuum flux of the source, (2) microlensing by stars in the lens galaxy, and (3) reverberation of the continuum by the broad line region (BLR). The latter, ignored by state-of-the-art microlensing techniques, can introduce high-frequency variations which we show carry information on the BLR size. We present a new method that includes all these components simultaneously and fits the power spectrum of the data in the Fourier space rather than the observed light curve itself. In this new framework, we analyse COSMOGRAIL light curves of the two-image system QJ 0158-4325 known to display high-frequency variations. Using exclusively the low-frequency part of the power spectrum, our constraint on the accretion disk radius agrees with the thin-disk model estimate and the results of previous work where the microlensing light curves were fit in real space. However, if we also take into account the high-frequency variations, the data favour significantly smaller disk sizes than previous microlensing measurements. In this case, our results are only in agreement with the thin-disk model prediction only if we assume very low mean masses for the microlens population, i.e. < M > = 0.01 M-circle dot. At the same time, including the differentially microlensed continuum reverberation by the BLR successfully explains the high frequencies without requiring such low-mass microlenses. This allows us to measure, for the first time, the size of the BLR using single-band photometric monitoring; we obtain R-BLR = 1.6(-0.8)(+1.5) x 10(17) cm, in good agreement with estimates using the BLR size-luminosity relation.