Recent scanning tunneling microscopy (STM) experimentally observed strong gap inhomogeneity in Bi2Sr2CaCu2O8+δ (BSCCO). We argue that disorder in the pair potential underlies the gap inhomogeneity, and investigate its role in the Fourier-transformed inelastic tunneling spectra as revealed in the STM. We find that the random pair potential induces unique q-space patterns in the local density of states (LDOS) of a d-wave superconductor. We consider the effects of electron coupling to various bosonic modes and find the pattern of LDOS modulation due to coupling to the B1g phonon mode to be consistent with the one observed in the inelastic electron tunnneling STM experiment in BSCCO. These results suggest strong electron-lattice coupling as an essential part of the superconducting state in high-Tc materials. © 2006 The American Physical Society.