OK no one answered me but here is my solution:
Running Startup Repair 3x did not work. Neither did FixMbr and Fixboot.
Simple instructions for geeks:*Plug in ONLY the Windows drive
*Double check that it's the Windows drive...Seriously. This was my mistake.
*Type Bootrec /RebuildBcd at the Repair Console command prompt. (See below for safer backp method)
*Reconnect the additional drives
*Delete or move the boot files on the additional drives via the Repair console. (They are C:\bootmgr, and C:\boot\bcd.) ***Type Dir first to make sure you're not in the Windows partition.
*Reboot into the BIOS and make sure the hard drives are booting in the right order.
Voila!
Comprehensive Safe(r) Instructions:
*Note: this solution is not for Dual booting systems -- just single boot into Win7 or Vista.
First make sure the correct hard drive is plugged in. Embarrassingly, this was how I got into this mess.
(I.T. geeks always ask themselves "is it plugged in," every step of the way.) After unplugging the other drives, verify you have the right Windows drive in your BIOS -- hold down the Del or F2 key (check your boot screen if not.) If you can't tell by reading the drive's name, see if you can find where it tells you the size. Still can't tell? Move on to the next step.
--To unplug a hard drive, shutdown, unplug the computer from the wall -- the whole power strip. Press the power button for 20 or 30 seconds to discharge. Then open up your computer and, on the back of the hard drive, just unplug the single-colored cable only. Don't bother with the multicolored one with bundled wires. That's for power, and would be fine too but it's usually tighter and more difficult.
With only the Windows drive plugged in boot into the Repair disk and go to the Command Prompt. Verify you're in the write disk and partition by typing C: then type DIR. Is Windows listed? Does it look like your C: drive? No? Go to another partition by typing D: or E: or F: ...etc., then DIR until you find Windows. (See **Note below if your drive letters are changed.) No Windows? Wrong drive! Shutdown and connect another. Mine was on C:NOW TYPE:
C:
cd boot
attrib bcd -s -h -r
ren c:\boot\bcd bcd.old
Bcdedit /export C:\Bcd_backup
Bootrec /RebuildBcd
Now you need to delete the boot files on the other hard drives or things will be a mess again. Shutdown and reconnect 1 drive at a time to avoid confusion. Disconnect the Windows drive just in case.
Reboot without the repair disk to test if there are boot files on the drive. If you get a "operating system not found" message there are none and you're virtually done! Skip down to ~Almost Done!~ If you get a bcd message again like, bcd/ "winload.exe is missing or corrupt," there are boot files to delete.
Reboot into the repair command prompt again. Find the partition with the offending boot files on it by typing it's letter followed by colon, such as C: then type "cd boot" without quotes. The command prompt will change to C:\Boot>. If it says it cannot find the path, then there is no boot info on that partition. Try another letter. If no partition other than X (your repair disc) has a boot folder you're all good. Move on to the next hard drive.
**Note: the drive letters in the Repair console will be different. This is why I encourage disconnecting the Windows drive to avoid confusion and mistakes. Your C: drive may look like your G: drive, and your M: drive may be missing. Don't freak out! It's only temporary. The partition letters will be in order starting from C:, so C:, D:, E:, F:, and X: will be be your repair disk drive. It will ignore your custom drive letter changes like M: and V:.
Assuming you've found the boot folder on drive C:\boot TYPE:
attrib -s -h -r C:\boot\*.*
ren bcd bcd.disabled
cd..
attrib -s -h -r boot*.*
ren bootmgr bootmgr.disabled
OPTIONAL
attrib -s -h -r bcd*.*
move boot*.* C:\boot
move bcd*.* C:\boot
ren C:\boot C:\Dont_Boot
(For the simple but messy method skip the optional steps.)
DANGEROUS METHOD TO SIMPLY DELETE:
cd..
attrib -s -h -r boot*.*
attrib -s -h -r bcd*.*
attrib -s -h -r C:\boot\*.*
move boot*.* C:\boot
move bcd*.* C:\boot
rmdir C:\boot /s
~Almost Done!~ Now shutdown and disconnect this drive. Reconnect the Windows drive again ONLY, in order to get it to say Drive0. Restart into the BIOS and make sure it's Drive0. Press F10 and Y and shutdown.
Connect all of your drives. Restart into the BIOS and ensure that Windows is still Drive0, Then go into the boot options and make sure that the Windows drive is the first Hard drive to boot. You can leave the CD as the first boot device as long as the Windows drive is the first actual hard drive.
Remove the repair disk from the DVD or USB port and restart.
YAAAAAY!
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