Ha..ha..ha..I know this is not funny at all. I have this mac pro early 2008 for more than 6 years and it is still working hard till today.
Did you guys check the two small buttom battries that sit quietly on mother/ logic board, usually unseen behind the graphic card? Mostly, this is the main culprit! I had some experiences with the s/s above that being resolved after replacing them with the new one. To be safe, replace them every 2-3 years and check its surface contact for any sign of humidity or oxidation.
The 2nd possibility is new inserted RAM or maybe the RAM is death. But this rarely cause the symtoms you describe above. Just check on system information about RAM.
Then, this one is not easily solved or tracked. You may have accidentally download/ run incompatible software (software conflict) or deleted the important one. Just think what you have done recently with your Mac and search the culprit one by one.