This study describes a procedure that found a balance between the ability of polymer-stabilized nanorods (NRs) to self-assemble and the creation of narrow gaps to make reproducibly bright surface-enhanced Raman scattering (SERS) nanorod dimers. NRs were end-functionalized with polymers, which enabled end-to-end self-assembly of NR chains and control over inter-rod separation through polymer molecular weight (MW). We found a way to quench the self-assembly, by phospholipid encapsulation, reducing the polydispersity of the aggregates while rendering them water-soluble. This reduction in polydispersity and preferential isolation of short-chain nanorod species is important for maximizing SERS enhancement from nanorod chains. We prepared NR aggregates that exhibit ∼5-50 times greater SERS intensity than isolated rods (and ∼750× greater than bare dye) depending on inter-rod separation, when using Oxazine 725 reporter molecules. Colloidal stability of NR aggregates and temporal stability of the SERS signal in water were observed for 110 days. With enhanced SERS intensity, water solubility, and stability, these NR aggregates are promising optical probes for future biological applications.