A modified theoretical model of photon echoes (PE) in low-temperature doped glasses based on the tunneling two-level system (TLS) and stochastic sudden jump models has been developed. The distinguishing feature of the model is its adaptation for Monte Carlo technique. The developed approach is more general than usual PE theories and allows us to take into account the different microscopic parameters of spectral dynamics in doped amorphous solids: in particular, the minimal radius of interaction between TLS and chromophore molecules, the dispersion of this coupling constant, and the changes of matrix properties nearby chromophore (shell-effect). The developed theory was applied for calculations of two-pulse PE decays for an organic amorphous system with typical parameters. It was found that the slope of temperature dependence of the homogeneous line width is decreased with an increase in the above-mentioned minimal radius. This effect could be one of the main reasons for the discrepancy between some PE experimental results versus calculation using standard PE theory.