I've been trying to get clover working for me here too, I have a GA-X58A-UD3R Rev 2.0 (FH) with a i7-950 and gtx 460rv2. Been Running pretty strong since SL, and am currently running 10.9.5.
That being said, I decided to try to make a bootable clover usb just to try booting from clover and seeing how that worked. So far I think there have been problems with the r 88 version of clover, so I think it's best to use 76 till that's sorted out. My progress: I can boot with a bootable usb only if I partition it with the MBR partioning scheme and not a GUID/GPT one. If i partion with a GPT scheme I get the bootaf0: error upon booting that usb. My guess this is something cause with how it reads the mbr? I'm just posting to get my foot in the door so to speak of my progress, but I'll come back with more info.
Edit: I gave it another go, this time I used Unibeast to install Yosemite on a spare harddrive I have in my computer. I Booted Yosemite via my unibeast usb and then installed clover onto the reformatted efi partition of that drive, which seemed to work partly. I could boot to the clover boot menu, but then never got it past [pci configuration begin] no matter what bootflags I threw up. Though I'm probably missing some things out. I'll probably go over my config.plist again tomorrow, compare it to the base ones included in Tonymac's clover tutorial. Weird thing is sometimes it hangs for me when I try to boot with unibeast too so i'm not completely sure it's a clover problem. Alas I have a few more ideas to try.
An added note, when installing clover I don't think any of us with this motherboard need to install drivers in the 64UEFI section of clover, as I understand it these drivers are only loaded for UEFI boards, and since ours are only bios based boards they are probably pointless to have. We just need to worry about the 64bit drivers. Of course I could be completely wrong about that! I would be more than happily corrected by someone who knows more than me (of which there are plenty).