Both disks ripped to separate folders. Run DVD Shrink and click 'Re-author'. Using the right panel, browse to the first DVD folder and load the files. Drag 'Main Movie' from right to left pane. Repeat for the second DVD. You now have two titles in the left pane. Edit > Preferences to DVD-9 and backup to a new folder.
There will be a noticeable break between the two titles. For seamless playback you gotta merge them with DVD2One.