OS X El Captain Keychain Access "CommCenter wants to use the keychain" on start up, possible to merge keychains?

Problem: I have 4 logins for Keychain Access. Every time I restart my computer I get the message 4 times: "CommCenter wants to use the keychain for login_keychain1, login_keychain2, etc." , and I have to enter my password each time. I can log into Icloud.com, Itunes store, Macbook, everything, fine.

Hardware: I am on a MacBook Pro (Retina, 15-inch, Mid 2015), El Captain 10.11.3

Started: about 2 months ago when I upgraded to Iphone 6s Plus.

What I have tried: about every solution I can find on the internet. A lot of times tried repairing the keychain (while that was still a feature). I've tried starting fresh with a new keychain. I've tried using only one of the 4, I will get notifications every 30 seconds or so using my computer. I've tried deleting all the keychains (bad idea). I think the Comm Center has something to do with my external monitor, but I'm not sure?

One or two of the keychains have Security Certificates on them (seems like I would not want to delete these). Of course they are the oldest keychains.

If someone could please help.

Additionally I cannot log into my Settings -> Icloud panel on Macbook for a period of longer than 30 seconds. It will sign in, and then quickly sign out. I think this may be because one of the keychains has a password I must have set 4 years ago, and was resurrected somehow when I got the new Iphone/El Captain upgrade on Mac.

I don't remember it, and although I know the answers to the security questions, they are coming up wrong, AND to compound the issue my recovery email is a former work email address from a company I stopped working at 3 years ago.

I work on my computer at least 12 hours a day, I've been trying to fix this for several hours a weekend every weekend for the last 8 weeks.

I am familiar with terminal commands, ubuntu, etc. If someone could give me a solution, technical or non-technical, it would be greatly appreciated. I have also considered switching to 1p, I don't know if that would help.

I just don't want to "rm -rf" the wrong file, as I have a lot of important projects on my macbook. Please help!! What the problem looks like in Settings -> Icloud, and Keychain Access:

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