It's interesting. I don't think I ever really had a problem getting passed the boot screen. I'm not super technical, but my hypothesis is that the combination of the version of clover and el cap are "kinder" to issues of compatibility than passed bootloader/OS combinations.
For me, all that I had to do was create the clover unibeast usb with the legacy bios selection. Then boot verbose (which is mainly cuz I got bored since that initial progress bar was taking so long) which took me straight to the installer. I then first reformatted my drive, then ran the install and then the computer went to restart. And that's where an "issue" was in that it doesn't have the kexts (I believe) to take care of things like shutdown and restart. So the bootloader and processes stopped but the computer didn't actually shut down so I had to do it manually. Again, not a big deal as I'm not necessarily planning on having many intentional shut downs or reboots. I digress, so when I restarted the computer, I again booted from the usb but this time I booted (verbose) into my internal ssd with el cap just installed. Then went through all the regular setup processes and voila, I was in. After that in the post installation process is where I really started having my challenges.
TL;DR- The installation of 10.11.5 ran like you usually would run it and I was able to boot into El Capitan.
Please help...
