You have to boot from diskettes until the NT-part is fixed.
Now you have to peel the bootsector from your Linux-root-Partition. With /dev/hda2 as your linux-partition, the dd-command is:
# dd if=/dev/hda2 of=/bootsect.lnx bs=512 count=1
There is something wrong if your bootsect.lnx has more than 512 bytes.
Now copy the file bootsect.lnx to a DOS-formated floppy if this is your way to transfer files to the NTFS-Windows-partition.
You can copy it with
# mcopy /bootsect.lnx a:
or with
# mount -t msdos /dev/fd0 /mnt
# copy /bootsect.lnx /mnt
# umount /mnt