Yosemite crashed and my default boot drive is not visible

I installed Yosemite with no problems, but while playing a game my 2009 Mac Pro crashed, which has never happened before. On reboot, it now seems to be booting from a secondary internal drive, which is essentially a clean 10.9 install. My SSD, which was my main drive, is no longer visible. It can't be seen from Disk Warrior 4.4, Disk Utility, or under the About this Mac system report.
I have a Time Machine backup, on an external drive, from this afternoon, but it is not configure for the "new" boot drive. I am not sure how to use it to overwrite this drive. Maybe I should have posted this in the Time Machine forum, but I thought the Yosemite crash was the important point.
Any Ideas on how I can recover my old drive or restore my backup on my secondary drive?

I am up and running again. I removed my SSD and replaced it with an older drive that I had removed when I put the SSD in. The old drive could not be seen on reboot, but the SSD could be seen through a USB port. I assumed this meant my SATA controller had a problem. I decided to reinstall the SSD in the empty optical drive bay. Int he process I had to remove the 2 OS X hard drives, the one that booted in bay 2, and the one that could not be seen in bay 1. I also reinstalled those 2 drives. Bay 3 and 4 have windows drives.
Upon booting all three OS X drives could be seen. After giving them all unique names, I was able to boot back into Yosemite. I have no idea what was wrong. Was it the OS, the drive, the SATA controller? All seem to be working now.
Lets see what happens when I try to play my game again!

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