I'm getting an error saying somehing about vertices > 60000? What's causing this?

This is as far as I know a Unity bug, I can unfortunately not do anything about it. It seems to trigger when raycasting a lot or drawing a lot of gizmos.
It helps sometimes to turn of Draw Unwalkable Nodes or disable Show Graphs altogether.
[Update] According to what I have heard, this is now fixed in Unity 3.5.3J

Can the Free version be used in a commercial project?

Yes it can! Go ahead!
But consider purchasing the Pro version if you make money on it to support the development of this project as I have worked quite a lot on it.
A credit is never wrong either ;)