From your description, you installed Vista on the second drive, which meant the boot files were placed on the primary drive. Torrent G suggested you remove the primary drive and do a repair to the secondary drive.
You can only boot to an active partition. One thing the repair option does not seem to be good at is making a partition active. I would suggest you download a partition manager, such as Partition Wizard, and booting to it to make sure the partition containing the boot files, or OS, is active. Partition Wizard has changed their website, so look for a bootable, free version to use to burn and boot to so you can make the partition active. Once it is active, the repair options work much better. A Linux version, GParted...