Have you tried using the Partition Builder to replace your files? Sometimes you have to do that, especially when adding new files to the ISO.
On a side note, changing the game ID will NOT affect the save data; the custom ISO would still use the same game data as the original.
I actually have used Partition Builder on brawl before. Sadly, it did not work with a different ID. When I used WiiScrubber to change the ID the hard way, it did not work until I changed it back to RSBE01.
I never really knew a lot about IDs until I looked up the complicated way of changing them, and I know now that changing the ID will not change the save unless you change the boot.bin(or whatever it is). I actually want it to not use a different save though, so that's okay with me.

I just want it to be on my hard-drive the same time a different brawl is. (And I also maybe might be releasing this maybe with different versions for brawl+, brawl-, BBrawl and stuff

MAYBE)