Well, I fixed it the one way that I was almost 100% sure would work: I got on msdn and downloaded the 3.7gig iso for vista x64, boot to that, got to the command prompt, and did bootrec /fixmbr, bootrec /fixboot, and bootrec /rebuildbcd.. I'm not sure which one does the trick, probably one of the first two, but either way, it took Grub completely out of my startup, and I was able to unplug the second drive. Thanks for digging up those links, though, it still seems like there should be a way to do it from within Vista, but maybe not.
A bit of trivia for anyone who cares: Adaptec does not have drivers for Vista x64 for their ubiquitous AHA2940 UW SCSI PCI controller card. As a result, the secondary drive that has linux on it would never ever power down and could not be controlled by ACPI. I'm not 100% sure that it would have worked even with a driver, but I think it did work correctly when I was running XP x64. I only use Linux on this machine every once and a while just to mess around, so I don't need that 10k scsi drive heating up my chassis the rest of the time, ESPECIALLY since it won't power down automatically. But the stinkin' linux Grub boot manager installed onto the MBR on my sata drive with Windows, but when grub runs, it reads config files from the scsi drive, so grub would fail if I unplug the scsi drive. As a result, I couldn't get Vista to boot either. So my 10k scsi drive was only running a boot loader, which seems.... excessive
Anyway, thanks again for all the links.. except the 4th one in the post above this.. why would I want to get rid of vista?

I actually really really like Vista. I seem to be one of the few, but I always hated XP, and I love Vista, especially x64.. runs games and everything, smooth as silk.