Think of it as you need to overlay an edge weighted graph on to runescape. How you do that is up to you. I have made a couple of tools to autogenerate the graph, and manually generate the graph as well. Personally, mine is at least 95% autogenerated, then I go back and add manual nodes as needed.
So first make an edge weighted graph and make a tool to build one using runescape variables (x, y, z, etc.).
Once you make a graph (just make a small one at first), then you should make a pathfinder to be used on your graph. A* is obviously the widely used one in games. You then need to apply A* to the graph you coded/built and find a path from point A to B.
Last you need to create a walker that can traverse the path you feed it using your pathfinder, handling obstacles, cross plane traversal, dungeons, etc.
The way you store everything is up to you, but always keep efficiency in mind.
All I have to say is good luck. :p