AAAH!! Finally! You're my hero! I've been struggling with this problem for months now (those months seemed like years, actually). At some point I was too afraid to shutdown or reboot my MacBook because it got me too annoyed. I just couldn't handle the pain anymore. I almost accepted the fact that this problem was never going to be solved and that I should have lived with it until the end of time (yes, that's how pessimistic I got). Today I plannend my final fixing session. If it wouldn't succeed I just had to accept this terrible problem and live in agony, I told myself.
I poured myself a good cup of coffee, put on some music to relieve a bit of stress and started debugging, again. Not much hope was left in me, but after a while I found this topic. Because I had tried a ton of 'solutions' I wasn't very optimistic at first, but when I clicked 'Restart...' after upgrading to MySQL 5.7.17 (from 5.7.13) I felt the adrenaline (or the third cup of coffee) all over my body. The screen faded to black instantly, as usual. Normally the waiting then starts, but now, my friends, my MacBook finally rebooted, and quickly! In the blink of an eye!
The feeling of relief I'm experiencing now is hard to describe, I think this is already the best day of this year. I still can't believe this just happened. Again, thanks so much!