Hmm... I'm trying this out now, and it appears to work jsut fine, specials and all... I have modified files, however.. I put shadow on top of donkey kong instead... the fit().pac is proabbly where the problem lies. with the up-b action it calls for an item specific to Sonic, in his slot, there are still a few things that aren't in brawlbox or psa that are references to other files that really can't be changed without modifying commons...
However, there is a quick fix to this... take the shadow and put it on donkey Kong and sonic on sonic of course. it worked for me, but I'm not sure what shadow you're using.