So you have a custom index.php page and all the other files are vbulletin files? Just make sure you don't upload the vbulletin index.php page and replace yours. Or, you can create a /forum directory (name it whatever you want), then close your forums, change the Forum URL (vboptions > Site Name/URL > Forum URL) to yoursite.com/forum, then move all the vbulletin files into the /forum directory.
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