Thanks. It worked. Just to detail out to those who faced similar problem. What i did was
1. Install latest Gnex toolkit v9.0
2. Launch it, choose the version of my Nexus which is option 6, android 4.1.1 (build JR03C)
3. Choose option 6 (Flash recovery (CWM Touch, TWRP Touch or Stock)
4. Choose option 3 (Flash Stock Recovery)
5. Put my phone into Fastboot mode and click continue
6. Once done it will auto reboot to phone
7. I then go to Settings>Apps>All>Google Services Framwork and click clear data
8. Go to settings>about phone>update and click check update
9. It shows update to 4.1.2 available and now I am able to do OTA update to 4.1.2.
Thanks again to Vernon. I hope with this I have go back to stock rom and in the future update I can still do OTA.