A two-stage scheme is presented to study structural perturbations of the sine-Gordon equation. Although the method is based upon the inverse scattering transform, detailed knowledge of this technical apparatus is not necessary in order to effect the calculations. In the first stage, slow modulations of speeds and positions for the soliton components are computed. The radiation resulting from the acceleration of the solitons is then calculated as a first-order correction through an easily constructed radiative Green's function. The method is exemplified by using it to study several outstanding problems that arise in applications of the Josephson transmission line. In particular we consider: (i) the pinning of flux quanta by microshorts, (ii) the quantum flux shuttle, (iii) annihilation conditions for fluxon-antifluxon collisions, (iv) breather decay, and (v) radiation from a moving fluxon.
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