First freeze any app you want to get rid of and run the phone for at least a few days. If it gives you problems, unfreeze it and don't get rid of it. It's a lot less work that backing the app up, changing it to a user app, uninstalling it, then having to reinstall it and changing it back to a system app.
As far as rooting, if you can't root using adb, you shouldn't be rooting the phone. You have no idea what a "one click root" is doing in addition to leaving you rooted. People who rooted the AT&T Note 3, then unrooted it, still couldn't get the 4.4.2 update - there were changes made to the system in addition to rooting it. Unrooting it didn't reverse those changes.