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Try this: take the animation MenSelmapPos_TopN__1 from mu_menumain, and put it into your common5. Then run UpdateMenuMain. That should let you keep your My Music layout. (MenSelmapPos_TopN__0 controls layout for the normal SSS.)

Well, that didn't fix my problem XD
But you gave me ideas on how to fix and I did figure something out :)
Here's what I did: I just took the old mu_menumain.pac and replaced the MenSelmapPreview.pat0 file in AnmTexPat(NW4R) with the one that was in common5.pac so I didn't have to update the whole file (and screw up other stuff at the same time).
Thanks for the reply anyway :)

...it can do a lot of things, like change which MenSelmapMark entries point where...

Thank you so much for this :D

However I've been having a bit of a problem. Using the stage manager program to change these (MenSelmapMark) only updates the SSS (not the "my music" menu) and using the "UpdateMenuMain" program you posted screws up the textures and alignment of the other buttons in the "my music" menu (I'm using Project: M, so the button textures and position in common5.pac are different than the ones in mu_menumain.pac).
Do you have any idea how I could fix the MenSelmapMark icons (and MenSelchrMark too) in "my music" without messing with the other stuff?