Computational approaches to the analysis of collective behavior in social insects increasingly rely on motion paths as an intermediate data layer from which one can infer individual behaviors or social interactions. Honey bees are a popular model for learning and memory. Previous experience has been shown to affect and modulate future social interactions. So far, no lifetime history observations have been reported for all bees of a colony. In a previous work we introduced a recording setup customized to track up to 4,000 marked bees over several weeks. Due to detection and decoding errors of the bee markers, linking the correct correspondences through time is non-trivial. In this contribution we present an in-depth description of the underlying multi-step algorithm which produces motion paths, and also improves the marker decoding accuracy significantly. The proposed solution employs two classifiers to predict the correspondence of two consecutive detections in the first step, and two tracklets in the second. We automatically tracked ~2,000 marked honey bees over 10 weeks with inexpensive recording hardware using markers without any error correction bits. We found that the proposed two-step tracking reduced incorrect ID decodings from initially ~13% to around 2% post-tracking. Alongside this paper, we publish the first trajectory dataset for all bees in a colony, extracted from ~3 million images covering 3 days. We invite researchers to join the collective scientific effort to investigate this intriguing animal system. All components of our system are open-source.