2008 MacPro upgrade to Maverick; problem with wake up.

IT runs like a well oiled machine when it runs. But, it has a problem finding the start up drive. I keep getting the flashing question mark quite frequently. I have to unplug the power cord and leave for 5 minutes EVERY time i start up.
I have initialized my HD and loaded Maverick on a blank drive; I have held down the S key for safe reboot and many other actions. But the only thing that seems to work is unplugging it.
It all started when I upgraded to Maverick. First my memory modules that came with the machine went out. I replaced them by rearranging the other ram I had installed. I don't know if there is any correlation between these events or not.
Was wondering if there is a computer command equivalent to unplugging the power cord for 5 minutes?? replacing battery??

2008s are fussy.
Pulling the plug is asking for trouble. Resetting the SMC may not really help but should be done.
Zeroing out a new drive and cloning your system with CCC and do a checksum on copy operation.
zap pram will require going to Startup Disk in control panels, set it there.
Safe boot is okay but Recovery mode is better, and repairing the drive in two places, top level and system volume.
But booting from another drive at least then you can do more and reformat a drive.
FBDIMMs fail, today they are cheap, better and run cooler just look on Amazon for Mac Pro FBDIMMs, you can use 667 which are usually cheaper, or 800MHz.
While at it, invest in a SSD for the system, best $139 upgrade and performance.

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2008 MacPro upgrade to Maverick; problem with wake up.

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