The Flatland Challenge, which was first held in 2019 and reported in NeurIPS 2020, is designed to answer the question: How to efficiently manage dense traffic on complex rail networks? Considering the significance of punctuality in real-world railway network operation and the fact that fast passenger trains share the network with slow freight trains, Flatland version 3 introduces trains with different speeds and scheduling time windows. This paper introduces the Flatland 3 problem definitions and extends an award-winning MAPF-based software, which won the NeurIPS 2020 competition, to efficiently solve Flatland 3 problems. The resulting system won the Flatland 3 competition. We designed a new priority ordering for initial planning, a new neighbourhood selection strategy for efficient solution quality improvement with Multi-Agent Path Finding via Large Neighborhood Search(MAPF-LNS), and use MAPF-LNS for partially replanning the trains influenced by malfunction.