Quasi-one-dimensional YSi(2) nanostructures are formed via self-assembly on the Si(100) surface. These epitaxial nanowires are metastable and their formation strongly depends on the growth parameters. Here, we explore the various stages of yttrium silicide formation over a range of metal coverages and growth temperatures, and establish a rudimentary phase diagram for these novel and often coexisting nanophases. We identify, in addition to previously identified stoichiometric wires, several new nanowire systems. These nanowires exhibit a variety of surface reconstructions, which sometimes coexist on a single wire. From a comparison of scanning tunneling microscopy images, tunneling spectra, and first-principles density functional theory calculations, we determine that these surface reconstructions arise from local orderings of yttrium vacancies. Nanowires often agglomerate into nanowire bundles, the thinnest of which are formed from single wire pairs. The calculations show that such bundles are energetically favored compared to well-separated single wires. Thicker bundles are formed at slightly higher temperature. They extend over several microns, forming a robust network of conducting wires that could possibly be employed in nanodevice applications.