Hey Mr. Lee, what exactly are you trying to achieve?
If it's disabling flash as a plugin, this is a good start, http://krypted.com/mass-deployment/deploying-and-managing-google-chrome-the-rough-guide/ then look at http://www.chromium.org/administrators/policy-list-3#DisabledPlugins

Basically, I'd like to disable the Google built in Pepper Flash and use the standard Flash Plugin.

Matt:

You understand that this is not supported by Google and may not even work? That Chrome is a 32-bit app and the "standard" Flash Plugin is 64-bits on modern hardware? That the "standard" Flash Plugin is currently broken on some Mac hardware: http://forums.adobe.com/message/6296305

Very interesting. Its a company policy so let me pass that info on. Thanks Greg!

All that said, disabling the Pepper Flash Player and enabling the player in /Library/Internet Plugins using this technique: http://newtriks.com/2012/12/01/how-to-disable-the-chrome-pepper-flash-player/ seems to work. Not sure how you'd do manage that on all your machines, however.

Yeah thats the hiccup, its a JSON coded preference file.

"its a JSON coded preference file"

Which is editable. Plenty of JSON modules for various scripting languages. But you need to do it for every user at login, so that probably means a LaunchAgent, and figuring out the needed edits, etc.

I know the portions to edit. Now its just figuring out how.

Perfect place to use Python...