I'm looking into this myself.. luckily only 1.7 to 1.7 however.
So far my plan is to simply clone the git repo of the base code I started from, branch the code, commit your changes to the branch, upgrade the base, then merge my changes.. well, thats what I'm trying to do, haven't succeeded yet, still reading the git book. ;-) Seems sound right?
At least it should show you everywhere you have changed, and you might not need to make all the changes in the next version. If they have drastically changed things, you might have to rewrite your mods.
Git cheat-sheet: http://stackoverflow.com/questions/315911/git-for-beginners-the-definitive-practical-guide(http://stackoverflow.com/questions/315911/git-for-beginners-the-definitive-practical-guide)
Git book: http://git-scm.com/book(http://git-scm.com/book)
