We present an improved analysis of halo substructure traced by RR Lyrae stars in the Sloan Digital Sky Survey (SDSS) stripe 82 region. With the addition of SDSS-II data, a revised selection method based on new ugriz light curve templates results in a sample of 483 RR Lyrae stars that is essentially free of contamination. The main result from our first study persists: the spatial distribution of halo stars at galactocentric distances 5-100kpc is highly inhomogeneous. At least 20% of halo stars within 30kpc from the Galactic center can be statistically associated with substructure. We present strong direct evidence, based on both RR Lyrae stars and main-sequence stars, that the halo stellar number density profile significantly steepens beyond a Galactocentric distance of ~30kpc, and a larger fraction of the stars are associated with substructure. By using a novel method that simultaneously combines data for RR Lyrae and main-sequence stars, and using photometric metallicity estimates for main-sequence stars derived from deep co-added u-band data, we measure the metallicity of the Sagittarius dSph tidal stream (trailing arm) toward RA~2h-3h and DE~0{deg} to be 0.3dex higher ([Fe/H]=-1.2) than that of surrounding halo field stars.