The ability to redirect electron transport to new reactions in living systems opens possibilities to store energy, generate new products, or probe physiological processes. Recent work by Huang et al. showed that 3D crystals of small tetraheme cytochromes (STC) could transport electrons over nanoscopic to mesoscopic distances by an electron hopping mechanism. Such protein-based structures with multiple localized electron carriers are promising materials for nanowires. A potential barrier to protein nanowire adoption for handling long-range electron transport is that fluctuations at room temperature may distort the nanostructure, hindering efficient electron transport. To study these fluctuations at the nano- and mesoscopic scales, we carry out classical molecular dynamics simulations for a small fragment of a STC nanowire and measure the effective distance distribution for electron tunneling. From distance distributions, we develop a graph network representation for electron transport along nanowires with varying dimensions, and through stochastic methods determine the maximum electron flow that can be driven through these STC wires. Longer nanowires were capable of carrying less electron flow than shorter nanowires with the same diameter, as long electron transfer distances that occasionally arise reduce the efficiency for electron transport. Thicker nanowires permit more alternative transport pathways, increasing electron transport beyond the increase in cross-section. Thus, this model implies that the design of protein-based nanowires that depend on electron hopping between charge carriers must consider control of the inherent protein flexibility, as more flexible protein-protein interfaces impose a limit on the required minimum diameter to carry currents commensurate with conventional electronics.