I can think of a couple things to check:
1) Not all SATA drives will work with that motherboard. Did you check the versions against the list at http://www.intel.com/support/motherboards/server/s5000vsa/sb/CS-022697.htm ? I have never seen untested drives become damaged, but I have seen them not be detected
2) When you put the new drives in, did you disable the onboard RAID first? If not, the motherboard may still be expecting the old drives, and not presenting the new ones properly to the 2008 install.
3) You should still be able to access the System Event Log (SEL) even with no HDs attached. You can run http://downloadcenter.intel.com/Detail_Desc.aspx?agr=Y&DwnldID=18949&ProdId=2487&lang=eng from DOS, and see if any hardware issues are reported.