When you reset the CMOS, did you go back in and redo the BIOS settings? If not, that is why the hdd is not detected, I bet.
As for it not loading into the OS, put the card back in and remove the drivers from the hardware mgr and then shutdown, remove the NIC and see if everything is ok. It sounds like a bad driver, to me compounded by bad BIOs setup after the CMOS flash.
I hope this helps.
Dave