OS X El Capitan keychain login cannot be found to store

Upgraded to El Capital 10.11.3 yesterday, at the last prompt where it asks to login using iCloud I supplied my user/pass and then it sent code to my iPhone which I typed correctly but after that it just froze there and continue button never enabled

So at this point I had to do hard reset to get access back

after that since my first login

Issue
a. When trying to use System Preferences > iCloud > login with my id
I get an error saying "keychain login cannot be found to store "
b. Just tried to add a Wi-Fi password and got error saying "Keychain System cannot be found to store"--- so it seems keychain in general is broken or impacted
c. I use Internet Accounts > Google Accounts for Contacts > every now and then i get notification on top right saying Google Password Required, no matter how many time I enter it keeps saying that message

What i have tried so far
1. went to ~/Library/ and then moved Keychains folder to my desktop, Rebooted so it would recreate the keychain again but this didn't
2. earlier I had Two Step authentication enabled on my iCloud id so i disabled it

The very same iCloud account works fine on other OS X and iOS so I am sure my account is okay

Solution 1:

not sure if this means anything but i deleted all system keychains and restarted. I had to re-enter passwords for wireless and re-get certs for company wireless but it worked. Keychains are the bain of my existance some times.