Dear anglicana, from reading the entry in Wikipedia, I can only imagine that the author has invented some word to describe the vehicles used by the Authority. It might be some sort of space ship or time machine or something like that. I think only the author knows the true meaning.
I have no idea what “shiftship” means, but maybe go to Wikipedia and look up “The Carrier”. I interpret the second sentence such, that a shiftship is a spaceship capable of moving through the space between alternate universes, so I assume it has the ability to shift from one universe to the other and the name might be derived from this.