Vibrational modes play a key role in characterizing metal-molecule-metal junctions, but their detection currently either requires single-molecule sensitivity or the generation of defect-free large-scale junctions. Here we demonstrate that surface-enhanced Raman scattering (SERS) on nonideal surfaces can provide a significant amount of information despite many defects in the layer. We determine the vibrational signature of the molecular electronic junction for palladium ions complexed and reduced on 4-mercaptopyridine adsorbed on rough gold and gold nanoparticles using SERS and density functional theory. We show that these nonideal surfaces can be used to probe kinetics of metal ion complexation and establish the success of electrochemical metallization. SERS on nonideal surfaces is thus revealed as a useful tool to rapidly establish the key process parameters in making molecular electronic junctions before embarking on more detailed studies on single molecules or single crystal surfaces.