Boot fails with grey Apple screen on Mac Pro 5,1

I have a 2009 Mac Pro 4,1 which has been flashed to 5,1 running 10.7.5 from an OWC 256 GB SSD, with a 500GB internal drive for data and another 2TB drive partitioned as Time Machine drives for boot and data drives. It has been running trouble free for 3 or 4 years mostly in this basic configuration, which has only undergone the regular Apple OS patches and installations of several well known programs from the Mac software canon, like DEVONthink Pro Office, Filemaker Advanced, CS6 a few others. It went to sleep the other night and I found I couldn't wake it after a few hours. I tried a hard power off and when I restarted got a light grey startup screen with Apple, after the spinning startup wheel disappeared prematurely. Moving the cursor and clicking the mouse resulted in a colored spinning ball that never stopped. I tried hard restart and resetting PRAM to no avail. Was able to start in safe mode and saw everything seemed to be intact, but opening Time Machine revealed that settings apparently had been lost as preferences showed it had not been set up. Several diagnostic utilities (Disk Utility, DiskWarrior 5, Drive Genius 3) reported that all disks were fine. I rebuilt directory with Disk Warrior 5 and this didn't help; things were same. Probably should not have done that but DiskWarrior is pretty safe. What happened and more urgently how do I fix this? Weirdest thing is that no disk or file problems were found and in fact disks were all in optimum condition. Thanks for any insights.