End-to-end capacity is a useful metric for network applications such as traffic engineering, QoS verification, peer-to-peer file distribution, video/audio streaming, admission control, etc. Although several tools have been developed to estimate end-to-end capacity and available bandwidth in wired networks, estimators for wireless adhoc networks are still to be developed. The paper briefly describes the model of a new capacity estimation tool for wireless ad-hoc networks. Then, it discusses two critical aspects in the implementation of any estimation tool: time stamping packets and clock synchronization. The paper details how to time stamp packets under the Linux and Windows operating systems, and a describes a regression-based mechanism that eliminates measurement errors due to clock drifts. The time stamping methods and the regression algorithm are implemented in the capacity estimator, which shows accurate capacity estimations.