I'm a newbie to rooting also. I did the CF auto root twice and had no problems. I also had the same problem as you. Device showed binary count increased and then device status Custom. Both times I unrooted, had the same problem as you. On XDA developers site I found the answer. It's a lot of work, which is why I don't want to root anymore. Go to Sammobile site and find the firmware for ICS for the N8013. download the Zip and extract all the files. There should be a .tar file after you extract. That is the file you use to Flash via Odin. First though, root your device again. Once rooted get the Triangle Away app in the Play Store and use that to reset the Binary Counter, Binary Status to Official, but mine didn't reset the Device Status to Official.
What you have to do is then Flash the U.S. ICS file for the Galaxy Note N8013, then Do a Factory Reset and Data Wipe, then once back to ICS, you can then download 4.1.2 again either OTA or Kies. I had to do this a couple of times. First time when going from the German 4.1.1 JB back to U.S. ICS, just to get the U.S. 4.1.2 when it came out. The factory reset and wiping is what takes so long. The other day after trying to Root to get the Multiview Manager to use any app in the Duel View on my Note, I decided to go back and unroot, because the main app I wanted in dual view wouldn't work. I did triangle away app and everything reset, except Device Status was still Custom. So I had to Flash ICS again, which Made device status "Official" and then reload the U.S. JB 4.1.2. So a lot of work, had to set up my GN again, but now I know how to root and it's easy, just don't really need it. Here is a link on XDA to what I did.
You'll need to do Option 2, once you find the U.S. Official ICS firmware zip file on Sammobile.com
[FIX] Getting a N8013 on a German ROM Back to U.S. 4.1.2 [UPDATED: 16JAN] - xda-developers
Just be prepared though, I still had to do a factory reset and wipe the device. Also, both times I got hung up at the Samsung logo after flashing to ICS and rebooting. if this happens to you, Just hit the Power button for like 5-10 seconds, when the GN turns off, before it starts up again, hit Power and Volume up at the same time to get into Recovery mode, where you will see to do a factory reset and Wipe option. Choose that and when all done, everything should be back to normal on your GN. Hope that helps you. It worked for me twice.