Ok, so then do as Sirkura said here:
Use sc_secharacter.pac in PF/menu2 its the same file as in common5.
But, use the latest version of BrawlBox. For Project M 3.6, they encoded the .pac file differently, so the latest version of BrawlBox is needed to see anything other than it appearing to be empty. I know, because I actually ran into this before, and then I found out that you just need to use the latest version of BrawlBox and just look at this separate file for 3.6. For more details, click here.
Post Merge: February 10, 2017, 09:46:07 AM
I dunno. When you say that you replaced the icons, did you replace the CSSs(These will have colored backgrounds; in vanilla Brawl, they're blue backgrounds, in Project M, they're purple backgrounds, etc.), CSPs(They will have transparent backgrounds, which'll look like checkerboards in BrawlBox), and Stock Icons in the sc_selcharacter? If so, you should be fine on all regular icons, with the exception of BP icons, which are in pf->info->portrite, as individual files per portrait. And in case you're wondering what each of these abbreviations is:
CSS: Character Select Screen - This is the miniature icon in the character select screen, where you click on the box to select that particular character
CSP: Character Select Portrait - These are the different "skins" or "palette swaps" you can swap between after selecting a character
Stock Icon: Pretty sure you know what these are
BP: Battle Portrait - These are the portraits of the characters that appear in-game next to your health