You didn't give us nearly enough information to know for certain what is going on. You may be running afoul of the Kitkat SD permissions that limit apps to a single folder. Or you may have broken app paths, outdated cache information, simple corruption or even something else altogether..
Restore a valid backup if you have one. If not, then that is something that you should be doing in the future to avoid this type of problem. Some things to try in the alternative would be wiping the system cache from recovery mode. Failing that, go to the application manager in the settings menu and try clearing the cache and data for a given app. And failing that, reinstall the app.
If you have more serious issues that aren't resolved by the above steps, then it will be hard to discern what happened unless you can give us a detailed, step by step description of all the changes you made. A situation where a valid backup would be the best way to recover. If wiping the caches doesn't work, you'd probably be best to simply start over and write a full stock firmware image to your phone with Odin, followed by a factory data reset.