[eluser]missionsix[/eluser]
Well there are two ways that I would go about doing this.
The first, which you kind of mentioned, is to modify the vBulletin index template to include a wrapper around your forum index to add columns to the left and right side. Then, you would write a vBulletin plugin / product that would display whatever you wanted into those extra columns. This doesn't involve Codeigniter so its not really relevant here.
The other solution, is to use the vBulletin API to re-create the forum index in your center column. Basically you would have the forums run under a root directory, as I have stated above (/forums/) and then you would probably have to re-create a class to build the forum structure of the homepage from the database. After this is done, you would make separate Codeigniter templates used by the forum index to make a duplicate of the forum index.
Either way your going to have quite a bit of work on your hands. It really depends on the situation though. If I were doing this, and the majority of the site were to be based on a forum, i'd scrap the idea of using CodeIgniter for the index and maybe limit its use to special section of the site that might require user authentication.