So just to be clear you were able to get into recovery and flash superuser, and that is where you are having the problem right now? Or are you not that far yet?
If you are on 4.3 you will have to wait as Koush is working on getting superuser updated to work with some changes made to the system. More info here:
https://plus.google.com/u/0/110558071969009568835/posts/LtttyekSUoi
I will add a note to the OP acknowledging this and update as soon as I am aware that it has been fixed.
In the meantime I believe Chainfire's SuperSU has been updated with a workaround that, afaik, is currently working on 4.3. I prefer that people use Koush's app and wait for that, but I understand people have needs and so you can find Chainfire's thread here:
[2013.07.25] SuperSU v1.43 - xda-developers
The flashable zip download is under the Play Store links. Please also be advised it's probably a good idea to check out the last few pages of the thread and see if anyone is reporting any issues at the moment.