After restoring your apps' settings, now most of your stuff should be good. Now it is time to restore your system settings. Run The batch Restore missing apps + system data as follows: Press uncheck all. next, scroll through the list - anything that syncs with Google account (contacts, GMail, Calendar, etc.) Do not check. You're looking for items that are in green - those are system items that can be safely restored, but you don't want to do all of the green ones - kinda taking a big chance. A few good ones are the following:
[BOOKMARKS] Browser
[CONTACTS/CALLS] Contacts Storage
[SMS/MMS/APN] Dialer Storage
[PLAYLISTS] Media Storage
[SMS/MMS PREFS] Messaging
Accounts
Application Widgets
[USER DICT] com.android.providers.userdictionary <-- (may not be there in your phone)
[VOICEMAIL] Dialer
All of the rest SHOULD be synced to and restored from your Google account automatically.
DO NOT RESTORE THE ONES IN RED AT ALL!
The ones in gray are application specific, so you can pick and choose any of those as well if you have the application back but its settings are still not there.