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I think you'd find modifying the vBulletin code straightforward if you are used to phpBB.
They have incorporated coding practices into their manual, showing you how to add your own custom coding.
Most of what you will do will never enter the actual PHP files. You will do a lot of editing in templates, including adding PHP code to them. These templates are stored in your database, so an upgrade doesn't affect your customization.
They have also incorporated an "if/else" method using a variation on XML style coding:
It's all pretty compartmentalized, pretty easy to tweak (endlessly.)