USB 3 not working on Yosemite MacOS 10.10.2
Have you tried resetting your SMC and NVRAM? Doing both of these can help solve not only this problem but other problems you're having with your system as well. 

See these articles from Apple.com for more details:
Intel-based Macs: Resetting the System Management Controller (SMC)
How to Reset NVRAM on your Mac