I have yet to play these new parts, but concerning the fall of Guardia, sure, you can go ahead. The basic description of what has to happen in that chapter is in the CE wiki. Concerning Dalton, well, he has built up a lot of hate for Crono's party in CT/CTDS and CE, so a battle against him in Guardia is kind of bound to happen. 3 times is not that much since the first battle against him in Chapter 1 is just a story battle that the player isn't meant to win. But if in the end that does look too much, we could always add one or two Golems in the 3rd battle against him, to make it very different (if it's not too broken in terms of difficulty!).