Just wanted to list here the steps i took to replace Grub boot loader with Windows Boot loader after migrating Wubi Ubuntu to a real partition (http://ubuntuforums.org/showthread.php?t=438591). I guess these steps are also applicable to direct Ubuntu installation.
Once rebooted after LVPM (migration to real partition that is), i noticed that Grub took over as bootloader. I did the following the restore windows boot loader :
1. Restoring MBR-backup, while preserving partition table (i.e. to allow booting into Ubuntu partion)
- copy MBR-backup to root : sudo dd if=media/host/MBR-backup of=dev/sda bs=446 count=1
----- This command simply means "raw copy input file MBR-backup only to the first 446 places of the MBR as 1 block.
- Rebooted and verified that Windows boot loader showed up instead of Grub's, booted into windows, and looked for for the presence of 2 files: Wubildr.mbr and Wubildr in c:\. Both of these file are installed by wubi installation and based on Grub4dos. Wubildr.mbr installed into master boot record and from there will look for wubildr and launch it. Wubildr look for and execute menu.lst. My understanding was that It will look first at root level, the whole partition and then the whole disk. Since the closest menu.lst will be the one inside wubi directory (c:\wubi/boot\grub\menu.lst), Wubildr will execute that and display Wubi menu instead of 'real' ubuntu menu. I had 2 options here, either to include 'real' Ubuntu within wubi menu, like tuxcantly suggested (http://ubuntuforums.org/showthread.php?t=438591&page=6) or to somehow make wubildr directly executes the 'real' ubuntu menu.lst. Opted for the latter; had wanted to uninstal wubi to recover some drive space that means no-more wubi menu.lst will be available, as wubi's grub directory will be deleted.
2. Copying menu.lst from the 'real' Ubuntu partition into the root directory
Within Wubi Ubuntu, I ran nautilus with root priviledge (sudo nautilus). i Browsed the real partition of Ubuntu and went into /boot/grub. Checked out menu.lst (Grub boot menu), by double clicking it (this launched a pop up asking for action, chose display, the file opened with gedit), made sure it listed reference to the 'real' ubuntu rather than to wubi ubuntu (look to text next to kernel should be /boot'... rather than /wubi/boot/...), made a backup copy of it (in gedit chose save as menu.lst.backup) and dropped a copy onto root (in gedit chose saved as menu.lst in filesystem/media/host).
Voila, upon reboot, i chose Ubuntu and it went straigth into 'real' ubuntu ( i left the time out option at 3 seconds and keep ubuntu menu hidden)
Now i am free to uninstall wubi ubuntu.
Hope this helps.... do leave feedback in any case.