Problems with mac pro early 2009

hi really need help here, i have had my mac pro since may2009 was working fine for 4months then it started to cut out intermittantly as if the power had gone off for a second, it would then reboot on its own. Have tried various things ie resetting SMC, zapping pram. The problem is it does this completely at random, after resetting the smc it lasted 2 weeks before it did it again. frankly its driving me nuts. I take it back to the apple store and explained what was happening the genius said that it may be a software problem and i should do a clean install before they take the machine in for checking/repair. The reason being that if it is found to be a software problem i would be charged. As i have a lot of projects on the computer it would be a real pain to do a clean install. i have 4 hd's in the mac one of which is clean with no data on it would it be possible to install the os on this drive to eliminate a software problem.If so i could then keep my main hard drive as is.

Thanks Steve