This research demonstrates registration algorithms specific to Inverse Synthetic Aperture LiDAR ISAL complex data volumes. Two registration approaches are considered, a mutual information registration algorithm MIRA and an enhanced, range bin-summed cross-correlation algorithm. For implementing these in the context of an ISAL signal, a theoretical mapping of the reflected target plane field to an aperture plane for multi-pixel detection is done. The theory for implementing both MIRA and cross-correlation enhancements is detailed and applied to a simulated sensitivity analysis that compares algorithm convergence and performance for different SNR, sub-aperture shift distances, and low pixel supports. To the best of the authors knowledge, this is the first application of 3D complex volume mutual information registration to LiDAR aperture synthesis. The enhanced cross-correlation algorithm showed significant gain in registration operability with respect to SNR and sub-aperture shift, giving new options for potential ISAL system design. An experimental Flash LiDAR system was constructed utilizing a multi-pixel temporal homodyne detection approach for simultaneous azimuth, elevation, range and phase imaging of target and this system was used to benchmark registration sensitivity for real data volumes. This is the first known application of a fast focal plane array for low support Flash temporal homodyne LiDAR for aperture synthesis.