Can you list the components please? Also is the hard drive on the primary IDE controller?
Never flash a CMOS unless you absolutely need to, all you did was put in a new case, should have nothing to do whatsoever with the hard drives.
Make sure that when you turn the system on that you hear the hard disk wind up, it will make a funny winding up noise (can't describe it better). If you hear nothing after you see the bios screen for autodetecting the hd then power off the case, unplug the hd and plug it into a different power plug off the power supply, repeat.
Finally u can dig out the manual for that hard disk and enter the numbers manually. Since you flashed the CMOS all your old settings are gone.