How to install bootloader to partition after install; use Windows bootloader to boot
 

I realize that since fedora 18, the installer no longer allows you to install the bootloader to a partition. However, I still wish to do this and add Fedora to the Windows bootloader along with Ubuntu (already installed).

I've already tried this method here in the second post: http://forums.fedoraforum.org/showthread.php?t=288304

chroot /mnt/sysimage
grub2-install --force /dev/sdXY

That appears to work, but it somehow messes with Ubuntu's grub installation to where I cannot boot into either OS. I just get dumped to the grub command line. I'm guessing there might be a way to fix this but I don't know how.

The way I add the OSes to the Windows loader is with EasyBCD. I manually select the linux partition (in this case either sda3 for Ubuntu or sda5 for fedora) and click "add Grub2 boot loader". This works fine for a single linux install along side Windows 7, but as I mentioned previously, I cannot boot two separate installs of Linux, each with their own boot loader.

Should I even be using grub to boot fedora on a partition if it is going to mess with ubuntu's installation? Should I try installing some other loader such as the FreeBSD loader instead so that there wouldn't be any conflicts? How would I do that?

I would just like to have two installs of linux along side Windows using the Windows loader. Unfortunately, Fedora's lack of options in the installer is making it difficult.

If I remember right, easybcd uses grub4dos and creates a \boot\grub directory and subdirectory/files in windows. I Think if you create entries in \NST\menu.lst for your linux distros should allow you to boot and/or chainload your linux distros from windows using the neo-grub entry.

I don't see how installing Grub2 on the Fedora partition could cause problems with Ubuntu on another partition unless you entered the wrong device/partition number. You indicate you are using EasyBCD and from your post, it seems the problems are there.

Did you run the command you posted at the end of the Fedora installation and before rebooting as instructed?
I don't use Fedora so can't test this but what I use to install Grub2 to a partition is the command below, the partition to install to being sda4. I do this from a Live CD and create the mount point /mnt/sda4 and mount the partition:

If that doesn't work you can try the force option:

You could also add a Fedora configfile or chainloader entry in the Ubuntu menu and boot Fedora with that if you are having problems with EasyBCD.

Alright I tried again, this time with only Windows 7 and Fedora on the drive; sda1,2 for windows and sda3 for Fedora. I ran this command:

grub2-install --force --root-directory=/mnt/sysimage /dev/sda3

/sysimage is where /dev/sda3 automatically mounted when I clicked on the drive in Dolphin so I used that. I did this after install on the livecd.

I then did the same thing I did to create the Ubuntu entry with EasyBCD - Grub2 Auto find Linux install. Unfortunately, when I select Linux from the boot menu, I just get dumped into the grub command line. I guess it can't find the kernel to boot or something? What exactly would I edit to make it work?

edit: did it again. Here is the output:

/usr/sbin/grub2-bios-setup: warning: File system ‘ext2’ doesn't support embedding.
/usr/sbin/grub2-bios-setup: warning: Embedding is not possible. GRUB can only be installed in this setup by using blocklists. However, blocklists are UNRELIABLE and their use is discouraged..
Installation finished. No error reported.

edit2: I chrooted into sda3 in the live cd and ran the grub2 config program and now it works. Now I got another problem though; after installing the Nvidia (gtx680) binary drivers from the repo, my mouse no longer works. I'm guessing it created a faulty xorg.conf? I tried removing it but then my system wouldn't boot.

edit3: Okay apparently there was no evdev config file in xorg.conf.d so I made one. I still don't unerstand why I need an xorg.conf because shouldn't I be able to run without one? I used nvidia without xorg in Ubuntu fine.