A "clean" install and keeping everything as is are incompatible. You are upgrading your computer which means things are gonna change. Even application specific prefs in some cases.
And without knowing what exactly you want to keep, it's hard to give advice. Adobe keeps things all over the place, for example. Other applications are much more tidy: move Application Support folders, prefs and the application package and you're good to go.
The safest and most efficient method would be to make a current backup, upgrade the Apple way, and then see if anything breaks. If so, fix those problems manually. Its usually pretty obvious, and easier than hunting all over for the files to manually move. I've migrated and the entire Adobe Master Suite and other messy stuff worked fine. Just had to enter a few serials.