You must have forgot to add the .pac files along with the .pcs files. .pac files are needed for any character that switches to another character. Try adding the .pac files for the various johto vertex hacks and I'm sure that they will work properly.
As for the codes, I really can't help you their. I know that Brawl+ has an individual PKMN code and Brawl- has it so that you don't switch mons when you die, but I don't know about using the code outside of those bigger hacks. Sorry.
Ok thank very much, you are a very big help X3