Followed the guide and now up and running. I have a little different config. I use a small 8 GB mSata for Clover boot and have my OSX installed on an RAID 0 via software raid. The only difference that I saw verses the instructions is that I did not see an extra boot option on the Clover screen and just selected my old Yosemite drive and El Cap installed without issues.
In order to avoid the monitor shutting off during boot, I disabled nvidia driver during and through the install. After installation was complete, I installed the modified AppleGraphicsControl.kext from the Yosemite patches and re-enabled nvidia drivers. This is the same thing that happens every time a new OSX patch is applied.
This is my second try. My first went the same but I got random reboots so rather than try to troubleshoot, I rolled back to Yosemite. I had the exact same issue on the second try, but I narrowed down the culprit to Safari. I disabled all the yellow flagged plugins and restarted and that seems to be the fix. 2.5 hours straight running and no random reboots. I thought it may be Safari because on my Macbook Pro, Safari would lock up and I would need to restart until I disabled those plugins.
Here is what works and what doesn't for now:
- All my USB ports work in 2.0. I can't get 3.0 speeds.
- Bluetooth works
- iMessage and iCloud work
- In Yosemite, I did not have all the speed step frequencies working. With El Cap, I got them all.
- On Geekbench, I am down about 15% on multi CPU benchmark.
- Finder is running slow and lagging. However, all my files may be getting reindexed.
- Power management still doesn't work but that was expected since there is still on x99 support.
I am staying on El Cap for now. I really don't need USB 3 so will wait to see if there is a simple solution.
10/25 Update - Tried to get USB working and completely blew up the install. Also prior to that, random reboot was not 100% resolved. Still had it happen a couple times, just not as frequently as before. Close but no banana so rolling back for good.
10/25 Update part 2 - I am stupid. Forgot to disable SIP when I was in the middle of changing my Clover config.plist. Also figured out that the random reboots was due to having the wrong ethernet kext. Back to 10.11.1 but unsuccessful in getting USB 3.0 going, but all ports working, just at 2.0 speed. Rather than kill myself, just going to buy and install a $30 USB 3.0 PCI adapter that is Mac compatible and give me another 4 ports.