So 10.11.2 came out, and I am still unable to log into Messages with iCloud on my Mac, though it works fine on my iPhone and iPad.
So I am on the phone with Apple Tech support. They for sure can see that my MacPro is not authorized. We went through signing out my iPad and iPhone of Messages, Facetime and iCloud and then signing back in, but that didn’t help.
I was then moved to a level 2 tech, who sent me and apple application called Capture Data, and had me try to log into Messages with it collecting packets, and I sent the info to Apple and they will be contacting engineers.
They were very nice and I am supposed to hear back Monday. Fingers crossed that they can figure this out. Seems like it has to be on their end, as it worked fine before El Capitan and the weirdest part to them as well is that it still happens on my clean install of the OS.