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Packet-pair based link estimation methods allow the estimation of bottleneck bandwidth in Internet routes. In practice, several complicating effects combine which can seriously distort such estimates. We provide a new delay variation based route model which allows the principles of packet-pair to be formalised and extended. This enables the effect of probe size to be evaluated, downstream noise understood, peak detection recognised as superior to mode or minimum based filtering, and new estimation methods to be proposed and evaluated. Using insight from the governing equations and simulation, it is shown how real measurements made over a 12 hop route can be interpreted. Unexpected additional probe size dependencies were found, inspiring an extension of the route model to include lower layer headers. It is shown how the enhanced model accounts very well for the observed dependencies, allowing more accurate estimates and a greater understanding of the role of cross traffic.