All USB ports working for five minutes after booting, then they all lose power except the front two USB 2 ports.

What gives?

I know there are thousands of threads on USB 3, but ive never seen one about all ports crapping out after initially working fine for several minutes. I'm running the latest release of 10.12 Sierra as of the date of this post.

MSI Z87-G-45 4670K GTX 1070

Booting through Clover. One thing I can't seem to get a straight answer for is which S/L/E to use. Some guides say the one in the Clover EFI partition. Some say the one in the MacOS install. Which is it? The same goes for the Clover config file. EFI partition or MacOS install partition?

Thanks!