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A Quantum Key Distribution (QKD) protocol describes how two remote parties can establish a secret key by communicating over a quantum and a public classical channel that both can be accessed by an eavesdropper. QKD protocols using energy-time entangled photon pairs are of growing practical interest because of their potential to provide a higher secure key rate over long distances by carrying multiple bits per entangled photon pair. We consider a system where information can be extracted by measuring random times of a sequence of entangled photon arrivals. Our goal is to maximize the utility of each such pair. We propose a discrete-time model for the photon arrival process, and establish a theoretical bound on the number of raw bits that can be generated under this model. We first analyze a well-known simple binning encoding scheme, and show that it generates a significantly lower information rate than what is theoretically possible. We then propose three adaptive schemes that increase the number of raw bits generated per photon, and compute and compare the information rates they offer. Moreover, the effect of public channel communication on the secret key rates of the proposed schemes is investigated.