Cognitive radio ad hoc networks (CRAHNs) constitute a viable solution to solve the current problems of inefficiency in the spectrum allocation, and to deploy highly reconfigurable and self-organizing wireless networks. Cognitive radio (CR) devices are envisaged to utilize the spectrum in an opportunistic way by dynamically accessing different licensed portions of the spectrum. To this aim, most of the recent research has mainly focused on devising spectrum sensing and sharing algorithms at the link layer, so that CR devices can operate without interfering with the transmissions of other licensed users, also called primary users (PUs). However, it is also important to consider the impact of such schemes on the higher layers of the protocol stack, in order to provide efficient end-to-end data delivery. At present, routing and transport layer protocols constitute an important yet not deeply investigated area of research over CRAHNs. This paper provides three main contributions on the modeling and performance evaluation of end-to-end protocols (e.g. routing and transport layer protocols) for CRAHNs. First, we describe NS2-CRAHN, an extension of the NS-2 simulator, which is designed to support realistic simulation of CRAHNs. NS2-CRAHN contains an accurate yet flexible modeling of the activities of PUs and of the cognitive cycle implemented by each CR user. Second, we analyze the impact of CRAHNs characteristics over the route formation process, by considering different routing metrics and route discovery algorithms. Finally, we study TCP performance over CRAHNs, by considering the impact of three factors on different TCP variants: (i) spectrum sensing cycle, (ii) interference from PUs and (iii) channel heterogeneity. Simulation results highlight the differences of CRAHNs with traditional ad hoc networks and provide useful directions for the design of novel end-to-end protocols for CRAHNs.