I have the same setup you do on all my systems, minus the empty SSD. The last time I migrated disks was when I installed SSD on two systems in 2011.
As you noted GRUB2 is fine. It sits above the partitions. I have Windows on my first partition and Linux on my second partition. I don't bother with the BIOS boot loader as hitting F keys to make a choise is a pain with my Asus systems...due to the BIOS password protection I have to enter a passowrd before I can select a boot option. But if I just let it boot to GRUB I can select what I want without needing a PW.
Anyway, the reason that windows is on the first partition is because that's where windows expects to be. (BIOS BL will get around this but still a pain for me.) Linux doesn't care where it is as long as you point the boot loader, GRUB, to the right spot.
When Linux breaks on the rare occation I use my live CD to boot and re-attach the OS to the loader. The help section under GRUB is fantastic for this. However for Windows it's more of a pain. I've had to re-install via DVD and when that's done it breaks GRUB by over writing the MBR. Then I have to do the above trick to fix/re-apply GRUB.
As I always have to look this up on search engines, I have no idea what I do with the bookmarks I save after each time, I'm not able to point you in the right direction at the moment.
My first question would be; Do you think that everything is fine and all you need to do is get GRUB2 to "see" the Windows partition? If that's the case you should be able to use which ever tool you use to install programs to re-install GRUB. That would be the fastest way and it should search and find everything automatically.
If Windows is damaged you're going to have to repair or re-install and then use a/your Linux live CD to repair GRUB due to Windows breaking it.
As it's late, or early in the morning, I might not be as clear in my discriptions as I think I am so let me know if you follow what I'm trying to discribe.
In this link follow the additional links to fix Windows and/or re-install GRUB. I haven't checked them all but it's a popular issue with only a few solutions.
Link - http://askubuntu.com/questions/228080/dual-boot-ubuntu-and-windows-7-bootmgr-is-missing-when-i-tried-to-boot-in-windo
Fixing a failed/bad GRUB re-install; http://askubuntu.com/questions/136390/windows-7-windows-8-entries-missing-after-reinstalling-grub
If you need the steps of how to re-attach the Linux OS to GRUB after fixing Windows let me know and I'll get the link from my Live CD to the help pages. It's easy to follow and only takes a little while.