1.: Clean up folders to not confuse Clover.
2.: Remove the old USB injector
3.: Update AppleALC.kext
4.: New USB method, which configures ports correctly
5.: Update the Audio ID for new version of AppleALC.kext
Also, if your GPU looks like the picture below, plug your DisplayPort into the port marked with red, this is mostly cosmetic, but will make the 2. stage of the Apple boot logo look nicer
View attachment 208342
If you want iMessage to work just follow this guide:
An iDiot's Guide To iMessage the config.plist already contains some values for all of these, but I purposefully did them in a way where iMessage does not work, as everyone should use their own values
Also, np I have been hacking away on this motherboard since december, so I know most of the things that can go wrong, but I hadn't seen your case before, always fun to learn something new.
I'm not sure but I think that the original problem was that the USB installer was somehow corrupted.
I don't know if you remember, but did you download the El Capitan installer just before starting the install or was it an older version (Anything before 10.11.4 would be causing problems).