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Sprite had a utility that I think still works but what it does is takes a snapshot before you do your upgrade then compares files after the upgrade and only restores those that were not part of the upgrade. I used it a couple of times accross ROM's and it seemed to work fine. The only issue is that if it missed something and restored an old file you might not figure it out right away but eventually you would find something that didn't work the way it should and that could be the problem. that never happened to me but i did hear of it by at least one person. worth a try though. the trick is that you have to do the first part BEFORE you do the upgrade or it won't work.
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