I thought I knew what you were looking for so I second guessed you. I figured you wanted to know weather it was worth your expenditure of time at this point, which is why I opted to give you the results in the above format. Unfortunately, I do not have the time to look at most of the files to give you a generalization or search terms, but would be happy to present you with some differences if you want to select a few files from that list. Most of the changes or summation are already outlined on the PHP site, under migration. The vBulletin changes I noticed, followed the guideline. I have a complete filtered list, but it will be less time consuming for you to compare your source to the original and makes changes accordingly. Creating a side-by-side compare list can easily be accomplished with file/text compare software, as you know. The company I work for generates their own code utilities, but if you need references to commercial utilities then I can suggest a few. They are not for the novice, as having a good understanding of filtering techniques is a must -- as would be expected.
As long as your specific, I am happy to provide you with whatever I know.