I already had Apple replace my logic board some 6-9 months ago. Actually, it had passed all the hardware tests that Apple ran it through. They were't obliged to replace it, but did so anyway.
All was fine until after the 10.11.5 Update... but the issue began again while using ServerPress. Not sure if ServerPress had anything to do with triggering it though.
Eventually, I gave up trying to use my second monitor and while the problems persisted it wasn't nearly as bad. I was able to put in about 4 days of work without the dreaded Freeze and Hellish restart process.
Safari had nothing to do with it. I turned off the "Allow Web GL" in Safari Preferences and the problems persisted.
Even though I knew the suggested 'Fan Fix' was out in left field, I tried it anyway. Didn't help. In fact, it seemed to make matters worse.
I also disabled the automatic graphic switching but it also failed to improve the situation. The problems continued to degrade. Instead of crashing every day or two, it began crashing every couple of hours.
I did several system reinstalls and finally installed El Capo on one of my external disks to use as a start up. Didn't help. In fact, the continuos crashes caused my external disk to fail. I've just reformatted it and am now resting data from the cloud.
Ok, because I was able to work without mishap in Safe Mode when everything else was bottoms up, I figured that the problem had to be related to an extension conflict.
So, I performed a clean install. Instead of using the migrated to move the apps over from my Backup Disk, I'm installing them all again.
So far so good. I'm now using both monitors again. The computer is behaving much better! It arrises from the system communicating with the monitor. S, I figure the problem is related to a dodgy driver. It may not be completely faulty, but is most certainly fragile.
Hope that helps