In this paper we probe surface enhanced Raman scattering (SERS) and Surface enhanced Fluorescence (SEF) from probe molecule Rhodamine 6G (Rhod6G) on self-standing Au nanorod array substrates made using a combination of anodization and potentiostatic electrodeposition. The finished substrates were embedded within a porous alumina template. By varying the etching time i.e. the thickness of the alumina, we show that there exists an inverse relationship between SERS and SEF. SERS and SEF also show a nonlinear response to increasing etching time due to an inhomogeneous plasmon activity across the nanorod. By modeling the electromagnetic fields created at different etching times we confirm the nonuniform plasmon activity along the Au nanorods and explain the nonlinear behaviors of SERS and SEF. Optimization of the level of alumina matrix thickness optimizes conditions for obtaining either maximized SERS, SEF or for simultaneously observing both SERS and SEF together.