MacPro Won't restart - clicking noise - full shutdown and start OK

I've been having this problem with my MacPro 1,1 for months. If I restart it will just hang there making a clicking noise until I hold the power button to force it to shutdown and then I can start it without any problem.
Recently I had a complete hard drive failure and used Time Machine to restore onto a new hard disk. Now I have a problem where sometimes it just sits there with a folder with a question mark on it showing it can't find the drive to boot from. If I hold down the alt key then it shows my disk but calls it EFI Boot, not it's normal name of Macintosh HD, but then it can start up fine.
So I'm not sure if I've got two problems or if my old problem just got worse, any other info I need to post to help diagnose the problem?

"EFI" is cosmetic and can be result of using Disk Warrior for one. I think the trick is to reset Startup Disk off and back to the volume.
And DO run Disk Warrior in addition to Apple DU to repair and rebuild the directory!

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