What I thought was "running fine" was while I had the USB still plugged in to boot... Once I took it out... no boot whatsoever. I made sure to copy the EFI clover folder to the EFI folder on the boot disk. Nothing.
So I actually got Vanilla El Capitan up and running on my system using the kexts you have linked and the screenshots from clover. Its up and running fine, but I can't get ethernet to work.
I had a windows disk for this computer, and tried to install SteamOS as well, and found out... My NIC is dead! But that's alright; I ordered an OS X compatible USB 2.0 to Ethernet adapter from Amazon, and it should be here in 2 days.