Welcome Mustang, sounds like you've had a real nightmare scenario there. At least you've managed to keep your XP installation without losing files
Microsoft have indeed removed Boot.ini in the latest beta version of Vista - there official statement reads:
"Windows Vista introduces a new boot loader architecture; a new firmware-independent boot configuration and storage system called Boot Configuration Data (BCD); and a new boot option editing tool, BCDEdit (BCDEdit.exe). These components are designed to load Windows more quickly and more securely.
The traditional Windows NT boot loader, Ntldr, is replaced by Windows Boot Manager (Bootmgr.exe) and a set of system-specific boot loaders. In the new configuration, Windows Boot Manager is generic and unaware of the specific requirements for each operating system, and each system-specific boot loader is optimized for the system that it loads."
Hopefully if you take a look at either BCDEdit.exe or Bootmgr.exe you'll find something that will help you edit the boot option menu. (If you've not already removed these files)
Remember to report back on how you did it if you manage to get it working....