It seems like we are dealing with two separate issues in this X58 centric topic. One is just the switch from Chimera to Clover and the second is upgrading to El Capitan. I think many of the issues here are a product of trying to do both of those things at once. There are a lot of variables and the resolution of issues that arise become more difficult to identify.
I have a
GA EX58 UD3R 1.6 (FK) with a XEON 5650 CPU. I have been booting using Clover since I installed Yosemite. I currently have a nearly perfectly functioning system booting with Clover to El Capitan. For me the upgrade was fairly simple, I was starting with a fully function Clover booting Yosemite OS. I think working out booting with Clover (into Yosemite) is a way to minimize the number of possible issues. I followed a Youtube video to create my first successful Clover boot. It was very simple and worked 1st time. All other tutorials I followed had failed to this point. I'll link to the video but want to emphasize that these BIOS boards must use Legacy Clover install which places an EFI folder in root directory. The video starts with UEFI install 'clover selections' and about 2/3 through shows the Legacy 'clover selections'. Follow the Legacy instructions. I should point out that the video is not in english but if I can follow it...anyone can. Here is the video:
Installing Clover Bootloader to HDD on UEFI or Legacy Boot
I had originally installed Yosemite using unibeast and then applied Clover post install. At that point I had to deal with:
•Fix Audio - used the Mulitibeast ALC888 legacy v100202 option in conjunction with optional EFI Installed Bootloader Support selection.
•Fix RTC CMOS reset issue (does not wake from sleep) - used this code to patch:
sudo perl -pi -e 's|\x75\x2e\x0f\xb6|\xeb\x2e\x0f\xb6|' /System/Library/Extensions/AppleRTC.kext/Contents/MacOS/AppleRTC
sudo touch /System/Library/Extensions
•Fix imessage - Followed the
Fix imessage thread and ultimately used the RTVariables method successfully.
My SMBIOS is set to MacPro 5,1. It matches my system the best.
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With that system in place and fully functioning I used Direct Update to OS X El Capitan Using Clover to upgrade to El Capitan. The issues I encountered were:
After initial install I had to use boot arguments -V, -f, -F , -X on first reboot to finish the install. Once the install finished I could boot normally (I made all changes to config.plist etc. as described in the "Direct Update to OSX El Capitan Using Clover" method).
I also had to:
•Fix Audio - used the Mulitibeast ALC888 legacy v100202 option in conjunction with optional EFI Installed Bootloader Support selection. I had to do this while booted to Mavericks on a separate SSD. A new El Capitan version of Multibeast does not yet exist and Multibeast for Yosemite would not function in El Capitan. I booted into Mavericks on a separate SSD I ran Multibeast fixes for audio and just pointed it to the El Capitan drive as the install location. It worked. The "audio_cloverALC-110_v1.0h.command" script did not work for me. It may be because I have my data drives and OS drives on different volumes...not sure but it did not work even though it did complete.
•Fix RTC CMOS reset issue (does not wake from sleep) - used this code to patch:
sudo perl -pi -e 's|\x75\x2e\x0f\xb6|\xeb\x2e\x0f\xb6|' /System/Library/Extensions/AppleRTC.kext/Contents/MacOS/AppleRTC
sudo touch /System/Library/Extensions
•Fix Disk was improperly ejected on wake from sleep issue - I have never had this one before. I'm using a free work around found here on this site:
SafeSleeper
So far I have had no other issues with this system.