I have finished my first trial run on this project, here are the results so far:
First: I ripped both of the discs with AnyDVD+CloneDVD set to DL size & preserved the menus, leaving out only one special feauture (the making of the movie.)
Next: I used DvdReMake Pro to merge the two discs (keeping menus), then exported the project to a folder on the HD, the size was 9.49gb.
Finally: I ran the resulting dvd files through CloneDVD set to DVD-5 size, preserving menus, quality at 41%, and now its ready to burn.
I have watched random chapters of the newly compiled DVD on my HD to preview it, all of the chapters work and it looks pretty good.