Patchy reionization leaves a number of imprints on the small-scale cosmic microwave background (CMB) temperature fluctuations, the largest of which is the kinematic Sunyaev-Zel'dovich (kSZ), the Doppler shift of CMB photons scattering off moving electrons in ionized bubbles. It has long been known that in the CMB power spectrum, this imprint of reionization is largely degenerate with the kSZ signal produced by late-time galaxies and clusters, thus limiting our ability to constrain reionization. Following Smith & Ferraro (2017), it is possible to isolate the reionization contribution in a model independent way, by looking at the large scale modulation of the small scale CMB power spectrum. In this paper we extend the formalism to use the...