Kogami,
If you can just use the sort order from the undub version I and ReviveDC made.
Use gdi tools to extract the sort.txt or use isobuster.
Dont use duplicates-once in mkisofs.
On disk 3 only use 2 cdda (leave the 2 second weird audio cdda out of it..) *this way motorcycle scene plays perfect
On disk 1 remember to use cdda to avoid heartbeats bar glitch.
Use all of the data excluding the speech files from the undub version I and ReviveDC made. (since people are saying some textures are glitched)
Open the ReviveDC undub in isobuster and view the start of 2nd session lba in hex.
Find the CD00 flags and hex edit to the correct lba that you prefer.
If you do this it shouldn't take more than an hour to have the undub completed and ready to be uploaded.
Also If you want to use the cinematic speech from my version feel free to do so.
I would say that all of the the cinematics in ReviveDC version are damn close to perfect. (maybe 98 percent complete) thats good enough.
The key is that your version has the complete undub of FREE Speech.
If you need the jap speech audio files I have all of them already downsampled.
Maybe try the -cache-inodes in mkisofs that comrade suggested?
-cache-inodes wrote: Cache inode and device numbers to find hard links to files. If mkisofs finds a hard link (a file with multiple names), then the file will only appear once on the CD. This helps to save space on the CD. The option -cache-inodes is default on UNIX like operating systems. Be careful when using this option on a filesystem without unique inode numbers as it may result in files containing the wrong content on CD.
If you do this your version should have no issues whatsoever.