Hey, thanks for the help but I got it sorted out.
What I ended up doing was to use the celltimes file that PgcDemux made from the DVD that ConvertXtoDVD created. That gave me VOBs/IFOs more or less identical to the ones I had before demuxing.
I then opened the newly authored DVD in DVDShrink and used its chapter cutting dialog to find the timecodes of the chapters as they were and where I want them—thanks to the previewer. Then I calculated the difference as number of frames and simply added them to celltimes.txt.
I used IfoEdit again to author the DVD again and bam! I had what I needed and was able to do the rest.
It took longer than I had hoped (about six days!) and it was much harder than I expected, but on the other hand, I learned quite a bit in the process, so I guess it was worth it.