After a buncha refactoring, some cursing and swearing I have progressed to... Plate pressure!
Red is for where plates are crunching together (So mountains and volcanoes will go there).
Green is where plates are diverging (depending on the plate type you'll either get lakes, or ridges like the mid-Atlantic Ridge)
Yellow is where not much of anything is going on.
That stuff is done using the dot product of vectors of each plate (Each plate has a unique movement). It's not 100% accurate but I don't think I need to get any more specific than this since the results look pretty good.
Still have to solve the plates having long fingers thing too... Argh.