I have used SPB to restore my phone with 2 new phones, and it restores EVERYTHING for me, including TF3D settings and all. Maybe there is something I am missing, but I did not notice any changes between my original phone (since Nov, 0
and this phone in terms of the settings that I have tweaked. There were certain modes of restore which caused my phone to not work properly, but I think it was the ROM upgrade mode which did the trick for me. I am not sure which, but it works great!