Hey, Gaius, nice mod! I skimmed it - it's a lot of JS, which I don't know very well - and it's cool. You should make a display video if you want to show off the differences between your mod and the standard.
I'm mostly interested in making the clustering / flocking behaviour without a formation more realistic, disregarding improving other aspects for now. In a strict implementation, I shouldn't have to actually end up modifying the costs of pathfinding though. Many more advanced crowd simulations are either based on a spring-force type model, or a velocity space model, and the path doesn't exactly change. The units will move a little differently, but their goal will be to move along the path, while the crowd simulation aspects (forces, velocity spaces, etc.) will keep them very slightly offset from the path. It should result in a better looking group movement without a formation.