This article introduces an augmented adaptive unscented Kalman filter (KF). The proposed novel technique is suitable to simultaneously estimate both the diagonal process noise covariance matrix and the unknown inputs, thus combining previously reported KF estimators for unknown inputs (dual or joint KF) and for covariance matrices (adaptive KF). A selective scaling method is also introduced to improve the convergence property of the suggested KF. The development of the novel KF is also motivated by a specific estimation problem related to crane systems. Cranes represent a special class of weight handling equipment as they are underactuated and described by nonlinear dynamics such that the load present oscillatory behavior. In addition to the increasing need for their automation in various industrial fields, these features also make them a benchmark system in control engineering with numerous control laws reported in the literature for sway elimination and trajectory tracking. A common issue to realize most of the advanced control laws on real, eventually industrial size cranes is the necessity to know the sway angle and frictions on the configuration variables. It is shown in simulation and also with real experiments on a reduced size overhead crane system that the suggested KF is suitable to estimate both the sway angles and the frictions.