I'm normally just a lurker, but I made an account to reply to this.
I've been encountering the same issue as I'm trying to finish my custom build for 3.6b. I think I've narrowed down the cause of the problem but haven't found a convenient solution yet.
In BrawlBox, you can find the pat0 mappings in
sc_selmap.pac>MiscData[80]>AnmTexPat(NW4R)>MenSelmapPreview
Then, you can find the franchise icon / MenSelchrMark (ie the mushroom for the Mario franchise or pokeball for the Pokemon franchise) in the lambert113>Texture0 directory.
Same goes for franchise logos (MenSelmapMark) in pasted_stnamelogoM>Texture0
You can modify the pat0 mappings there by renaming the MenSelchrMark.xx files to another number (ie MenSelchrMark.01 to MenSelchrMark.05 to change icon from Mushroom to Yoshi Egg for that stage). The files in Texture0 are assigned to the Stages by the SSS order, so just open Brawl Stage Manager and set it to view by SSS order and you'll have an idea for which stage's icon you're editing (ie the third entry --MenSelchrMark.01 corresponds to Delfino's Secret, and the next entry to Luigi's Mansion and so on in order from that point). Some stages are missing but you'll be able to figure it out if you cross-reference with Stage Manager's listed pat0 mappings. I think you should be able to edit the textures of the missing stages directly since they seem to lack pat0 maps altogether (these show up with red boxes around the images in Stage Manager) but I haven't tested.
Now the problem is that for whatever reason, when you edit a file under MiscData[80]>AnmTexPat(NW4R)>MenSelmapPreview, it immediately resets all the other files to null that you haven't expanded into view (under MenSelmapPreview). You can circumvent this by expanding ALL drop boxes in MenSelmapPreview as far as I can tell, but either way this method is painfully slow. It should work, at least.
Brawl Stage Manager seems to have a similar but not quite as severe problem, where it only nullifies SOME entries which is why you get the garbled SSS ingame. Unfortunately it seems that exporting and replacing directories is broken in this particular area in BrawlBox and it will either just import null entries regardless of what you export or just crash altogether, so that avenue is a no-go as well. So far the only solution I've found is that extremely tedious one I mentioned earlier.
Anyways, sorry if this is a bit incomprehensible; I'm an on-again-off-again tinkerer who has barely used BrawlBox at all and hasn't read any tutorials or whatnot, so this is just what I've been able to piece together myself from messing around with it (and as such I'm not sure if my terminology is accurate here but hopefully you get the idea).
TL;DR - Just read the post. There's a (admittedly mediocre) solution in there somewhere and maybe by reading it you can help find a better solution.
EDIT: Clarity