Okay so I will do my best to provide instructions to how to do it in this post but let me say you need time and patience. Also I had prior experience rebuilding a PS2 DVD9 iso.
This was done using a USA iso so I am not sure if it is different for a Europe iso.
What you will need:
1. Apache
2. CDVD Generator 1.5 or 2.0
3. Xpert 2.0
4. HxD Hex Editor or similar program
5. Rogue Galaxy v1.1 Plugin for Xpert
6. Rogue Galaxy USA DVD9 iso
7. Rogue Galaxy Director's Cut Japan DVD9 iso
8. Rogue Galaxy Undub DVD5 iso
You could potentially do without the undub DVD5 iso or the Japan iso but you need at least one of them and I would highly recommend it to be the undub DVD5 iso. Edit: It is actually best to have both the Japan iso and undub DVD5 iso because the undub DVD5 iso has the end credits removed which is a .MVI file and you can only get that from the Japan iso.
Steps:
1. Extract all the files from the isos into separate folders using Apache.
2. Open Xpert 2.0. Select the Rogue Galaxy v1.1 plugin. Select the matching .DAT & .HD6 from the iso files in Xpert and extract the LBA. After that is done you have to close Xpert and reopen it. Then select the plugin and files again. Then extract the files. You have to extract all the .DAT files in this manner but I would recommend you do them one at a time. Do this for the matching .DAT files in the iso.
3. After extracting the DATA0_0.DAT files for each iso then go into the extracted files and you will see a snd2 folder. You have to copy this folder with all the files inside from the extracted undub DVD5 or Japan files and overwrite the corresponding folder in the USA iso.
4. After that is done open Xpert again. Select the DATA0_0.DAT & DATA0_0.HD6 files for the USA iso and select rebuild. It will rebuild the .DAT file and save it as I believe NEW-DATA0_0.DAT. Then close Xpert and reopen it. Then select the NEW-DATA0_0.DAT file and the DATA0_0.HD6 file for the USA iso again. Select rebuild LBA. After that you will have a NEW-DATA0_0.DAT file and a NEW-DATA0_0.HD6 file. You now delete the DATA0_0.DAT & DATA_0_0.HD6 files and rename the new files as DATA0_0.DAT & DATA0_0.HD6. You can now delete the extracted DATA0_0 files for all the isos.
5. Now extract the DATA0_1.DAT files using Xpert for the different isos. Go into the extracted files and you will see two folders. These two folders both contain sound files but there is a wav folder contained within the eng folder that has a different number of files than the corresponding folder (named jap I believe) in the Japan files. But if you have the undub DVD5 iso it will have the correct number of files within it so you can just copy it over to replace the folder from the USA iso. The jap folder from the Japan iso has some files the eng folder from the USA iso does not have and vice versa. So basically just replace all the files from the USA iso with the ones from undub DVD5 iso.
6. Rebuild DATA0_1.DAT and Rebuild LBA using Xpert for the USA iso like you did before.
7. The files and folders in DATA1_0.DAT and DATA1_1.DAT are almost identical to the corresponding DATA0_0.DAT and DATA0_1.DAT files so extract them, replace the sound files with the ones from the undub DVD5 iso, and rebuild them like you did for the previous .DAT files.
8. Now copy the .MVI files from the MOVIE folder of the Japan iso or undub DVD5 iso and replace the corresponding .MVI files in the USA iso. Since the end credits were removed from the undub DVD5 iso the only place you can get that .MVI file from is the Japan iso.
9. Open CDVD Generator. Now select 'Create New Project' and the select the 'Dual Layer' option. If you are using 2.0 be sure to turn off 'Add Dummy Data' under options (I don't know if it matters but it does lower the size of the iso so that is a good thing). The 'Add Dummy Data' option will turn itself back on if you close and reopen CDVD Generator so keep that in mind. Now add the extracted files and folders from the USA iso by clicking and dragging them to CDVD Generator. In my experience the order does not matter but I usually do the folders last and the files in alphabetical order. You have to do this for both layers. Now select volume on layer 0 and under 'Disc Name' type 'SCUS97490'. Under 'Producer Name' type 'PLAYSTATION'. Under 'Copyright Holder' type 'SCEI'. Now save it and name it whatever you like. Select 'Rec' for record and another program will open after some error boxes. Select 'Export Image' and it will create image files split into four files *.000, *.001, *.002, *.003. You have to combine them using copy /b in command prompt, or AF7 Merge, or HJSplit should work too but I have not tried it personally. Do this for both layers.
10. Open HxD and open the layer 1 (Second Layer) iso file you have just created. You have to delete the header off the second layer iso before combining it with layer 0. So under edit select 'Select Block' and now select 'dec'. Now select 'Length' and type '32768' for the length. Now click 'OK'. Now under edit select 'Delete'. It will warn you and after accepting it will delete the header. Now save it and exit.
11. I have found rebuilt PS2 DVD9 isos will not work on my CFW PS3 unless I replace the header on the first layer with the one from the original iso. So open HxD and the original USA iso and use select block like you did before to select the 32768 dec header. Now copy it. Open the layer 0 iso (First Layer) and use select block to select the 32768 dec header again and then select 'Paste Write' under edit. After that is done save it and exit.
12. Combine the two layers using copy /b, or AF7 Merge, or HJSplit.
13. Congratulations, if you indeed did it. It is ready to use now.
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Skelletonike:
