Project based Finder window presets
Apple's solution for this is to use Mission Control (if you need multiple desktops) and Finder Tags for each file/project.

From there, you can use finder's tag filtering and/or smart folders to assemble your views.

Also, saving these to your Favorites and removing things you don't use make quick access to these "views" possible across finder and other app open/save dialogs.

Lastly, look at Divvy to automate window placement - it's very scriptable and you might use LaunchBar or another tool to speed actions if spotlight isn't action oriented enough for your automation.