If I understand correct you just have 2 hard drives in your server and the sites happen to be on opposite hard drives. As long as you are only running 1 MySql for both sites you shouldn't have any issues. The path to your install is in the Config.php this Modification is just changing were a second site looks for User, PM, and session data.
Now I have not done this with 2 existing forums. I have only created a new forum to attach to my existing forum. You could still do it with 2 existing forums but it would take a little more effort since you would have to merge your userdatabase and some PM's would be lost unless you could merge those as well. I have no experiance in doing this so I am not sure I could be of much help
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