The problem is that the SuperSU/Superuser app will work fine and seems to grant access to read files in areas you normally need root for to read (eg data/data), however, if I try to delete a system app (like Facebook) with any root File Explorer after mounting system R/W it will fail to delete. I also cannot install things like Busybox using stericsson's tool as it will just fail. Other root apps like System cleanup do not delete either.
I did not have this problem in the 4.3 build (though I used the Docomo method with locked bootloader here).
Any ideas? Something to do with the SELinux??