Additionally, I sometimes get random reboots when viewing web pages with flash content on them in El Capitan, so used CCC to return a Yosemite install image to one of my boot drives. The pain about dual booting with Yosemite and El Capitan is that for Yosemite I need MacPro6,2 in my config.plist and for El Capitan, I need iMac11,2, otherwise Safari crashes. The work around was to put a second incidence of the Clover EFI boot partition on a USB drive and select which to boot from in the bios menu.
Interestingly, where I had found that El Capitan seemed speedier than Yosemite, reinstating a the clean Yosemite image, with roughly the same number of apps installed on both, and booting form it, Yosemite seemed particularly sprightly, too. All a bit unscientific because I haven't benchmarked but I was part way not looking forward going back to Yosemite but now feel comparatively happy that I did. I wonder if there are some differences in the latest Clover that are making the difference.
Re El Capitan and sleep. On suggestion, I tried changing the number of video ports in my clover config.plist but it made no difference to the black screen problem, in my case.