I tried CloneDVD (it's free for 30 days :D), and it works very nice. Output is compatible now. When selecting the extra's in the menu it plays a blank .VOB file. The only thing is that when starting the DVD it jumps back and forward to the removed parts, it would be nicer to just skip that, but I will try to remove that later with IfoEdit.
The downside of IfoEdit is it's documentation, there are some tutorials on certain subjects but some basic knowledge of the DVD format would be handy, but it is hard to find. Any links to articles would be great.
BTW, I have Nero and downloaded all the updates to get Recode. The result is a DVD which does't work, very strange. Maybe a Kill Bill problem.