Dirty updated from OmniROM to latest CM11, fixed permissions, and got crashes. Firstly crashed com.android.phone, I have removed some files and managed to fix it. After it I have tested a little and experienced other crashes: com.android.themes.provider (when trying to enter to any submenu of themes menu) and com.android.settings (when trying to enter cellular network settings) . What files should I remove to fix it? I tried to clear .themes.provider's folder and .settings' folder, it doesn't help.
A dirty upgrade is never 100% error free. You have to either fix permissions (worked out for me) or wipe data and reinstall everything. Also check the owner and group of all the files and folders, they tend to be different even on the same Android version.