Yosemite clean install startup issue

I did a clean install of Yosemite on a new WD 1T HDD. It will start beautifully from the usb, but once I put it back in the bay it will not start internally. On the 1 out of 30 attempts it occasionally starts, it is still not functional. I've tried resetting PRAM and many other tricks I read about. Still no luck. I'm working on it from the USB as I type this question right now. HELP!