As long as the ability changes aren't too drastic (or slow), you two are the only ones who've touched the stone thus far, so that can account for your new skillsets via plot reasons. Speed, meanwhile...I figure there'll be a bit of time while some things are sorted out in-game, plus there are two new characters (potentially) to introduce. So, as long as you don't take too long and/or undergo violent transformations, by the time character capabilities become a major issue again all the changes should be made.
My only major concern would come if the party changed so much it no longer had a coherent reason for working together, but that's not so much of an issue at the moment unless every single person redoes their characters.
