if manual you need to unhide hidden files so you can transfer them to the usb.
in terminal type
defaults write com.apple.finder AppleShowAllFiles YES
to turn it off change YES to NO
ok. can you update clover to latest release from here https://sourceforge.net/projects/cloverefiboot (chameleon, stolen and rebranded)/files/Installer/then test again.
also attach your EFI folder.
i see... ok what boot loader are you using if clover zip your efi. if chameleon i guess zip your extra folder and use the forum more reply option to attach it here
dude what bios version are you at i cant find it in all those pictures it looks like you took a picture of every page but the first one. A12 A13 A0? it should say on the first page in general info
did you do the bios downgrade then upgrade process. i think you have to go down to a03 bios then back up i am not sure if a12 bios is good to upgrade back too might be a11 if you search the forum its been mentioned a few times. JakeLo might remember off hand
you can read through this https://osxlatitude.com/index.php?/topic/7539-yosemite-installation-guide-latitude-e5440-intel-i5-clover-uefi/&do=findComment&comment=45927 hopefully it helps
i think that video card is similar to the radeon 5870 that i think works on mac pro. maybe you have to specify a frame buffer in your config file. maybe you can find something useful here http://www.rampagedev.com/?page_id=82