Visuo-haptic augmented reality systems enable users to see and touch digital information that is embedded in the real world. PHANToM haptic devices are often employed to provide haptic feedback. Precise co-location of computer-generated graphics and the haptic stylus is necessary to provide a realistic user experience. Previous work has focused on calibration procedures that compensate the non-linear position error caused by inaccuracies in the joint angle sensors. In this article we present a more complete procedure that additionally compensates for errors in the gimbal sensors and improves position calibration. The proposed procedure further includes software-based temporal alignment of sensor data and a method for the estimation of a reference for position calibration, resulting in increased robustness against haptic device initialization and external tracker noise. We designed our procedure to require minimal user input to maximize usability. We conducted an extensive evaluation with two different PHANToMs, two different optical trackers, and a mechanical tracker. Compared to state-of-the-art calibration procedures, our approach significantly improves the co-location of the haptic stylus. This results in higher fidelity visual and haptic augmentations, which are crucial for fine-motor tasks in areas such as medical training simulators, assembly planning tools, or rapid prototyping applications.