I'm no expert here, but you've definitely got to be careful with that 100mb partition. (It's a boot partition.)
If the 100MB Boot partition is on the 2nd drive, it's probably already in the wrong place. The OS may not boot with the 2nd drive disconnected, but if the configuration will tolerate it *Shrug* what works...works.
This will probably look like hell because it is getting pasted out of a .doc file (but I'm a bit pressed for time):
MS Boot Configuration Data Editor
For When Boot Fails Because the OS is Missing!
The following procedure is used to completely rebuild the Windows Vista, 7, 2008 boot configuration when it has either been badly damaged, or when restoring the OS to different hardware with a different disk/partition configuration.
1. Boot from appropriate OS media.
2. Select the current Windows installation if available.
3. Choose Command Prompt and run the below commands (some may be optional):
bootsect.exe /nt60 all /force
attrib -s -h -r C:\boot\BDC
bcdboot.exe C:\Windows /S C: /L en-us
Diskpart can also be used to mark a partition as active from the Windows RE.
SELECT DISK (followed by the number of the disk – most likely 0)
SELECT PARTITION (followed by the partition number – most likely 0)
Windows startup recovery should now work.