I would recommend that you start from a fresh install of the 10.10.1 (don't use 10.10.0) because I think you've "tried eveything" and something has gone wrong.
Remove your card, do a fresh install and get your system running on HD4600. Then, follow my instructions in Post #1 here. You can look at my H/Z97N guide (signature block) for reference (your audio and Ethernet drivers will be different), but run MultiBeast for Yosemite (v7.1.1) using the default MacPro3,1 System Definition.
BTW, (to all who are reading this) Apple's OS X has not supported VGA connections since Moses was a child. So, only use DVI or HDMI.