I did a clean install. I use DiskAid and that lets me see everything on my devices. I don't even have to have them connected with the wifi option. There's probably other apps you can do this with, but I love all the little features this program has.
So I basically made a folder on my desktop, and then offloaded all my stuff with a drag and drop. It asks you if you want the data too, and of course you say yes. Someone noticed that some games are registered to a unique ID, but most of everything I've tried doesn't have that kind of limitation. I've even done copies from one device to another.
I have never done a OTA except for the decimal updates. I've always done it like that with everything. I don't trust the installer to stall and screw everything up.