Awesome project, very excited to start building one!
Have you considered putting the RFID chip on a daughterboard so that it can be positioned in a small space that is removed from the main shield and Arduino? Maybe another type of coaster with jacks and cables? I see that SparkFun has a breakout board that I may use for an improvised version of this.
http://www.sparkfun.com/products/8423
-John