For anybody who is interested in the concept of verifiable voting protocols, and a real life election applying them, I am currently working on the front end of such an application, with the election to be held in November 2014 for our state election.
We are working with academics in Surrey, UK, and elsewhere on the cryptography and verifiability of the election. So I can't answer any of the hard questions, but can point you at some of the documentation that Surrey has developed, shown below.
Using Pret a Voter in Victorian State elections http://epubs.surrey.ac.uk/726039/1/EVT.pdf
Software Design for VEC vVote System http://www.computing.surrey.ac.uk/personal/st/S.Schneider/pa...