apparently your BOOT was actually on your old #2 HDD. BCDEdit bcdedit /set {bootmgr} device partition=C:
apparently your BOOT was actually on your old #2 HDD. BCDEdit bcdedit /set {bootmgr} device partition=C:
I'm certain Snuffy is correct. Put back your old #2 hdd and watch your system boot. This situation usually occurs when doing a clean install of windows and having more than one drive installed. I've done it to myself - sure was frustrating running all those bootrec commands successfully and still not able to boot. Windows: when it comes to installing, it's the ebola of OS's.
When installing Windows, don't use the entire drive. Leave some free space. I think it's 100MB for 7 and 350MB for 8. Then everything, including those pesky 'system' files, will be contained on the single physical drive.