A model is presented to analyze the spin waves scattering and ballistic transport at the iron-cobalt magnetically ordered alloy nanojunction between iron leads. The B2 structure considered for the ordered alloy with equal amounts of Fe and Co is bcc, where l=3, 7, and 11 for the number of (100) atomic layers between the bcc structure of the iron leads. To analyze the spin dynamics and spin wave scattering at the nanojunction boundary, the phase field matching theory is implemented in the Heisenberg Hamiltonian representation. The coherent ballistic reflection and transmission probabilities of spin waves from the iron leads incident onto the nanojunction boundary are calculated in accordance with the Landauer- Bfittiker description, and numerical results are presented for the ballistic spin waves transport across the nanojunction over the full range of their frequencies. The results are of particular interest for experiments for spin waves wavelengths greater than the nanojunction width. They demonstrate, furthermore, the possibility of the resonance assisted maxima for the spin waves transmission and reflection spectra owing to the interactions between the incident spin waves and the modes on the nanojunction, leading to inhomogeneous broadened Fabry-Perot type resonances, in contrast to other considered nanojunctions where localized modes give Fano type resonances. This effect is general and may be observed at different characteristic frequencies and corresponding incident angles. The eigenvectors of these modes are calculated for certain frequencies to illustrate the spin precession configurations of the representative nanojunction atoms for both the propagating and localized modes. (C) 2016 Elsevier B.V. All rights reserved.