We present 426 epochs of optical monitoring data spanning 1000 days from December 2003 to June 2006 for the gravitationally lensed quasar SDSS J1004+4112 . The time delay between the A and B images is \Delta t _ { \mathrm { BA } } = 38.4 \pm 2.0 days ( \Delta \chi ^ { 2 } = 4 ) in the expected sense that B leads A and the overall time ordering is C-B-A-D-E . The measured delay invalidates all published models . The models failed because they neglected the perturbations from cluster member galaxies . Models including the galaxies can fit the data well , but strong conclusions about the cluster mass distribution should await the measurement of the longer , and less substructure sensitive , delays of the C and D images . For these images , a delay of \Delta t _ { \mathrm { CB } } \simeq 681 \pm 15 days is plausible but requires confirmation , while delays of \Delta t _ { \mathrm { CB } } > 560 days and \Delta t _ { \mathrm { AD } } > 800 days are required . We clearly detect microlensing of the A/B images , with the delay-corrected flux ratios changing from m _ { B } - m _ { A } = 0.44 \pm 0.01 mag in the first season to 0.29 \pm 0.01 mag in the second season and 0.32 \pm 0.01 mag in the third season .