Originally Posted by Simon_Gardner
So there are only things installed 'off store' to worry about.
A factory reset as described will wipe your phone except for your media. When you restart and log into your Google account it will start downloading all the apps you have ever gotten from there, unless you disable sync. It is not an option for Google play store, but uncheking everything under settings>general>accounts>Google will stop it. You will (or should do) restore all your app data if sync is set to do so, not wise if you think your issues are to do with clashing app data. "Off store" apps will need to be reinstalled manually (side loading), stick the .apk files for them in a folder called apps on your external SD card and reinstall them from there. My guess is it is one of these that is causing you problems though.