We study how to use guidance to improve the throughput of lifelong Multi-Agent Path Finding (MAPF). Previous studies have demonstrated that while incorporating guidance, such as highways, can accelerate MAPF algorithms, this often results in a trade-off with solution quality. In addition, how to generate good guidance automatically remains largely unexplored, with current methods falling short of surpassing manually designed ones. In this work, we introduce the directed guidance graph as a versatile representation of guidance for lifelong MAPF, framing Guidance Graph Optimization (GGO) as the task of optimizing its edge weights. We present two GGO algorithms to automatically generate guidance for arbitrary lifelong MAPF algorithms and maps. The first method directly solves GGO by employing CMA-ES, a black-box optimization algorithm. The second method, PIU, optimizes an update model capable of generating guidance, demonstrating the ability to transfer optimized guidance graphs to larger maps with similar layouts. Empirically, we show that (1) our guidance graphs improve the throughput of three representative lifelong MAPF algorithms in four benchmark maps, and (2) our update model can generate guidance graphs for as large as $93\times91$ maps and as many as 3000 agents.