First, exactly what error are you getting? How do you know it can't locate the boot.ini? Was the error?:
Invalid Boot.ini
Windows could not start because the following file is missing or corrupt:
Windows\System32\Hal.dll
If so, there could be several reasons for that, and a missing boot.ini is only one of them.
Second, have you booted to CD and checked to see if the file exists on your C: drive (the default location)? If the file exists, have you examined the content to make sure it is correct?
Third, have you tried using the Recovery Console on the CD to restore the boot files?