Calculations are presented for the scattering and ballistic transport of spin waves (SW) incident from cobalt leads, on ultrathin ferrimagnetic cobalt-gadolinium ..Co][Co(1-c)Gd(c)](l)[Co.. nanojunction systems. The nano junction [Co(1-c)Gd(c)](l) itself is a randomly disordered alloy of thickness l hcp lattice planes between matching hcp planes of the Co leads, at known stable concentrations c <= 0.5 for this alloy system. To compute the spin dynamics, and the SW scattering and ballistic transport, this alloy nanojunction is modeled in the virtual ci:ystal approximation (VCA), valid in particular at the length scale of the nano junction for submicroscopic SW wavelengths. The phase field matching theory (PFMT) is applied to compute the localized and resonant magnons on the nanojunction. These magnons, characteristic of the embedded nanostructure, propagate in its symmetry plane with spin precession amplitudes that decay or match the spin wave states in the semi-infinite leads. The eigenvectors of these magnon modes are calculated for certain cases to illustrate the spin precession configurations on the nanojunction. The VCA-PFMT approach is also used to calculate the reflection and transmission spectra for the spin waves incident from the Co leads on the nanojunction. The results demonstrate resonance assisted maxima for the ballistic SW transmission spectra clue to interactions between the incident spin waves and the nanojunction magnon modes. These properties are general for variable nanojunction thicknesses and alloy stable concentrations c <= 0.5. In particular, the positions of the resonance assisted maxima of spin wave transmission can be modified with nanojunction thickness and alloy concentration. (C) 2014 Elsevier B.V. All rights reserved,