Mac Pro 3.1 with Yosemite won't boot after GenericUSBXHCI USB 3.0 .kext added
The problem was graphic card! GeForce 8800 GTS was making all that problems.
I have replaced it with Radeon 5770, and everything is fine!

Funny thing is, the USB 3.0 really has something to do with wireless magic mouse! USB 3.0 somehow interferes with bluetooth 2.4GHz waves!
It can be repaired with... aluminium foil!
I've covered bt module with aluminium foil, and mouse is working fine again!

Everything solved