All the Installer does is download the files anyways... AFAIK, you can use the Installer, copy the FS2 dir that it "installed" to, and merge that with your retail FS2 dir. That's what I'd try, IDK. Worth a shot.
You can always backup your FS2 dir before you do it.
Right-click FS2 dir, hit "copy", make a new dir "backup of FS2", open it, right-click, and "Paste", it will copy the FS2 dir for you.
If anything goes wrong, re-name or delete the FS2 dir that you played with, and then move the copy out of "backup of FS2".
Easy as pie, if you understand what I just described. If not, don't try it, you might mess something up.