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I finally got this down and made it. After the 3rd DVD of Kara no Kyoukai was released, there was nothing else I needed. So I sat down and started working. What I wanted was a single DVD disc containing the first 3 movies, along with the menus and specials. Therefore I had to use a double layer DVD9, and a little bit of demuxing and compressing.
 
First I demuxed the contents of each DVD using DVDdecrypter. Now I had the 6 M2V files, 12 AC3 files (stereo and 5.1 audio tracks). Next, I took out the menus, which I had to decompress from the original VOB using VirtualDub so I could easily manipulate them. Finally, I borrowed the english subtitles from gg's release (big respect and thanks). Oh, and I shouldn't forget about the main menu, which I made in Adobe After Effects (just a simple premade cloud/fog effect plus a track from the third OST).

Next step was the editing. I had pretty good experience with Sony DVD Architect from when I made a wedding DVD for our family friends, so I fired it up and looked at the possibilities. Well, it is a bit tedious to work with it sometimes, but generally it is a very nice peace of software. Creating menus, submenus, links, adding audio, video and subtitle tracks are all very simple (although I had problems sometime, but I learned quite a bit).

The worst part, as usual, was adding the subtitles. Architect has a neat function of importing subtitles, but they have to be in a special format. Good thing we have google, so I found out it has to be some weird MAC DVD Studio Pro format, which luckily can be found in Subtitle Workshop. So the steps were: open the .ass in Aegisub, export as .sub, open in Subtitle Workshop, export as MAC DVD Studio Pro... Phew.

What was really great about Sony DVD Architect was it's rendering. First, I optimized the DVD, which means it calculated how much compression would each item need to make the project fit onto 8.5GB of a DVD9. Then, it rendered for about 1.5 hours and voila. Now, I knew it would not end here, and of course I found some bugs, so I though - ok, I'll have to render again. But no, Architect has a neat feature of the 'preparation', where it can see what you changed in the project, and then render only those parts that were changed. This reduces the rendering time drastically. A real time saver indeed.
 
And so, I'm really happy that it worked out so nice. The loss of quality on the recompressed movies is unrecognisable, the subs are readable (although I'll be doing a test watching sometimes soon to be sure). When everything is alright, I might even release it out somehow...