There is no boot.ini in Vista. Vista uses BCD/BCDEDIT ( google it up )
When you recover Vista look at the links below
Here are some links on installing XP on Vista
http://apcmag.com/how_to_dual_boot_vista_and_xp_with_vista_installed_first__the_stepbystep_guide.htm
http://www.howtogeek.com/howto/windows-vista/install-windows-xp-on-your-pre-installed-windows-vista-computer/
http://forums.techguy.org/windows-vista/558994-how-install-xp-after-vista.html
EDIT: You did plug the HD's back into there original SATA ports ?
Sound like the drive with nothing on it may have had a hidden partition (recovery?)
In the Bios settings there is some times a HD boot order.
The BIOS reset is a jumper on the mainboard and can destroy the motherboard if you mess with it when the power is on
When you recover Vista look at the links below
Here are some links on installing XP on Vista
http://apcmag.com/how_to_dual_boot_vista_and_xp_with_vista_installed_first__the_stepbystep_guide.htm
http://www.howtogeek.com/howto/windows-vista/install-windows-xp-on-your-pre-installed-windows-vista-computer/
http://forums.techguy.org/windows-vista/558994-how-install-xp-after-vista.html
EDIT: You did plug the HD's back into there original SATA ports ?
Sound like the drive with nothing on it may have had a hidden partition (recovery?)
In the Bios settings there is some times a HD boot order.
The BIOS reset is a jumper on the mainboard and can destroy the motherboard if you mess with it when the power is on