You picked probably the hardest game to do. MSR had the worst copy protection of any game i can think of. I wrote a tutorial complete with instructions/ neccessary tools but due to legal reasons I dont think think i should link it without a "ok"
Heres why MSR isnt working: MSR (unlike all other DC games) checks ALL LBAs. Most games check the first file on the disc (1st_read.bin usually) which also contains its own location (11700). Thats why with simpler games the 1st_read.bin must be hacked but the other files can be sorted in any other youd like and the game still loads.
But MSR will verify the location of EVERY FILE. If you take MSR and change the location of a file it will not work. (Im referring to LBA location, the actually order of the files physically).
Example of the repack problem: suppose there are 2 files in MSR and thier LBA locations are 100000 and 200000. Now somewhere im between (lets say 150000) them is one of the music.afs files. You repack it and put it back in the exact same file order. Now the LBA of the first file is still 100000, the music file is 150000 but the other file is now 190000. What happened? The music file you created was smaller than the original, so the locations of all the files after it has been shifted thus making the game now NOT work.
The summary: to make a repack of MSR work
1- uses good audio tools
2- preserve the original echelon file order
3- the audio files (the afs files) must not push the rest of the files out of location
to meet the 3rd requirement, your audio repack must NOT be larger than the original, if its smaller it can be padded to the exact size of the original thus allowing the files to be found in the right spots.
Heres an older thread that details what im talking about.
Good luck.