Ultra-high energy cosmic rays (UHECRs, E>1e+17 eV) are the highest energy particles observed in the universe. Deflection in the cosmic magnetic fields makes it difficult to correlate these events back to their sources. However, the propagation of UHECRs reveals spectral features resulting from interactions with the CMB and EBL photons. We do a semi-analytical study of UHECR propagation, to obtain the primary and secondary particle yields on Earth and deduce general properties about their source class. A discriminator of mass composition models is derived from the ratio of the flux of individual neutrino flavors. For Sybill2.3c post-LHC hadronic interaction model, we improve the UHECR composition fit by incorporating contributions from two source populations. We have also studied the plausibility of particle acceleration in AGN jets through multi-messenger analysis using cosmic rays, neutrinos, and gamma-rays. Particularly some high-synchrotron peaked blazar spectra are better explained in the very-high-energy (VHE, E>30 GeV) range with line-of-sight resolved gamma-ray signals from UHECR interactions. The diffuse neutrino flux upper limits by the IceCube neutrino observatory In PeV-EeV energies can put constraints on this scenario. We calculate the neutrino fluxes from Fermi-LAT resolved and unresolved blazar population by simulating a luminosity-dependent density evolution. By and large, our knowledge of the UHECR source environment, candidate class, and energy loss processes are reinforced and we put forward blazar jets as potential candidates.