You should be able to manually delete the old Vista installation and boot files without a problem. Make sure you have the old drive disconnected while you're installing Vista on the new drive. Once you're done, you can connect the old drive again, take ownership of its contents, and remove what isn't needed.
It's possible that when you reconnect the old drive, the motherboard will go "oh cool, a new drive with a bootable OS on it! I'll make THAT the boot drive!" So on the first startup after adding the drive, you might want to go into the motherboard's BIOS menus and ensure that the newer drive is on top of the boot-device priority list. BIOS menus vary, so if you need help with this part, post what motherboard brand & model you have. Hope that helps
