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This paper proposes a general framework to effectively estimate the unknown timing and channel parameters, as well as design efficient timing resynchronization algorithms for asynchronous amplify-and-forward (AF) cooperative communication systems. In order to obtain reliable timing and channel parameters, a least squares (LS) estimator is proposed for initial estimation and an iterative maximum-likelihood (ML) estimator is derived to refine the LS estimates. Furthermore, a timing and channel uncertainty analysis based on the Crame??r-Rao bounds (CRB) is presented to provide insights into the system uncertainties resulted from estimation. Using the parameter estimates and uncertainty information in our analysis, timing resynchronization algorithms that are robust to estimation errors are designed jointly at the relays and the destination. The proposed framework is developed for different AF systems with varying degrees of timing misalignment and channel uncertainties and is numerically shown to provide excellent performances that approach the synchronized case with perfect channel information.