Discrete clusters of closely spaced Au nanoparticles can be utilized in devices from photovoltaics to molecular sensors because of the formation of strong local electromagnetic field enhancements when illuminated near their plasmon resonance. In this study, scalable, chemical self-organization methods are shown to produce Au nanoparticle clusters with uniform nanometer interparticle spacing. The performance of two different methods, namely electrophoresis and diffusion, for driving the attachment of Au nanoparticles using a chemical cross-linker on chemically patterned domains of polystyrene block-poly(methyl methacrylate) (PS-b-PMMA) thin films are evaluated. Significantly, electrophoresis is found to produce similar surface coverage as diffusion in 1/6th of the processing time with an similar to 2-fold increase in the number of Au nanoparticles forming clusters. Furthermore, average interparticle spacing within Au nanoparticle clusters was found to decrease from 2-7 nm for diffusion deposition to approximately 1-2 nm for electrophoresis deposition, and the latter method exhibited better uniformity with most clusters appearing to have about 1 nm spacing between nanoparticles. The advantage of such fabrication capability is supported by calculations of local electric field enhancements using electromagnetic full-wave simulations from which we can estimate surface-enhanced Raman scattering (SERS) enhancements. In particular, full-wave results show that the maximum SERS enhancement, as estimated here as the fourth power of the local electric field, increases by a factor of 100 when the gap goes from 2 to 1 nm, reaching values as large as 10(10), strengthening the usage of electrophoresis versus diffusion for the development of molecular sensors.