iCloud Issue After El Capitan Update 10.11.2 After updating my MacBook Pro to 10.11.2, I am having huge issues with iCloud. Thus far, I am noticing that:


I can no longer use Messages.





I cannot use FaceTime.





I cannot authenticate into iCloud via the Preference Pane.




I have verified my iCloud credentials elsewhere (on another Mac, on iCloud.com, on an iOS device).

Does anyone know how I can force iCloud to recognize my credentials on this machine?

EDIT: In response to the myriad suggestions by Tetsujin, I have catalogued them here:


NVRAM reset has been done.
Started up MacBook in Safe Mode.
CANNOT use Messages from Safe Mode.
Checked status of service (UP).
Signed out of Messages and Facetime on all devices and back in.
Restarted routers and incoming internet.
Tried alternate ISP.
Verified SN displays, and is valid.
Disabled all firewalls.
Checked veracity of /private/etc/hosts file.
Verified that no proxy was being used.
Deleted Keychain entries for imessage and com.apple.idms.
Verified that the Guest account CAN access Messages.
Deleted com.apple.apsd.plist and rebooted.
Reset SMC.
Reinstalled OS X 10.11.2.


None of these things has worked for me.

EDIT 2: I am also having issues running apps purchased via the AppStore. Each time I run one, I have to log into the AppStore to verify the purchase.

EDIT 3: I've done myriad changes including deletes of Caches, StartupItems, Libraries, etc. (in concert with AppleCare Support), and nothing has remediated the issue so far. I'll document everything as time permits.

EDIT 4: The issue is more than just with iCloud, but also involves certain apps that require access to some subfolders in ~/Library. For example, when I try to update EFI's Fiery Software, I get this:



And when I execute OmniFocus, I see this response:



And some apps that use the Sparkle framework to perform updates simply fail. iSale 5 is one example:



Some apps work fine, while others obviously do not. There is a major permissions issue here somewhere. I just haven't been able to track it down.
It seems that I have found the answer to this issue. I ran the ACL permissions repair tool at the Terminal in Recovery Mode, but when I checked the ~/Library and its subfolders from the CLI, I found that many of the subfolders were owned by another user account. (How this happened is anyone's guess.) The solution here was to Get Info for the ~/Library folder, and then ensured that I had RW access to it. Then, I simply chose to Apply to Enclosed Items...