So a little update, I think I fixed everything.
I decided to take the PCI E cable out of my EVGA GeForce GTX 550 TI Graphics Card. I left the card in, but now I was using the Intel HD Graphics 4600 Integrated Graphics.
I used my UniBeast Yosemite flash drive and booted up only using "-no-zp" (I don't know if I needed to do that or not, but it went through". Got to the installation screen, wiped the disc using disk utility. I was able to install Yosemite 10.10.3 no problem.
I restarted, booted up the Yosemite drive using "-no-zp", finished the installation screen. I ran multibeast and used the same settings I used in 10.10.2.
I installed the NVIDIA Cuda driver (7.0.36) and then I installed the NVIDIA Web driver (346.01.02f01). After they installed, I turned off the computer, reconnected the PCI E cable into the Graphics Card, and booted up the hard drive, not through the usb. It went through. The computer recognizes the Graphics card and everything seems to be working correctly!