How close is pirates to the HM building? Would there be enough room to add a darkride beyond the berm? Maybe even just a walkthrough attraction? Maybe a pirate stuntshow instead of Pirate Island. Something involving the Civil War (use the Lincoln AA), Mardis Gras, swamp boats...tons of ideas.
As for fitting the Train Station into CC, I would simply redo the Hungry Bear so the order/pickup is done on the bottom level and the train station is located on the top level with the majority of the station being on an extention to the back, saving most of the upstairs (minus train que) for additional eating space.