We present \emph{Chandra} monitoring data for six gravitationally lensed quasars: QJ 0158$-$4325, HE 0435$-$1223, HE 1104$-$1805, SDSS 0924+0219, SDSS 1004+4112, and Q 2237+0305. We detect X-ray microlensing variability in all six lenses with high confidence. We detect energy dependent microlensing in HE 0435$-$1223, SDSS 1004+4112, SDSS 0924+0219 and Q 2237+0305. We present a detailed spectral analysis for each lens, and find that simple power-law models plus Gaussian emission lines give good fits to the spectra. We detect intrinsic spectral variability in two epochs of Q 2237+0305. We detect differential absorption between images in four lenses. We also detect the \feka\ emission line in all six lenses, and the Ni XXVII K$α$ line in two images of Q 2237+0305. The rest frame equivalent widths of the \feka\ lines are measured to be 0.4--1.2 keV, significantly higher than those measured in typical active galactic nuclei of similar X-ray luminosities. This suggests that the \feka\ emission region is more compact or centrally concentrated than the continuum emission region. ; Comment: 55 pages, 22 figures