After a little experimenting, we have settled on me (the captain) 90 degrees minus one click ahead of the stoker.
The stoker found starting to be a little harsh at a full 90 degrees behind (something about me stopping the cranks at the bottom of my stroke). Overall, I would say we have picked up 1 to 2 MPH on the flats, and we're taking most hills in the middle chain ring (instead of the granny gear). We probably have not gotten any better at climbing, but I figure since we're out of phase, I am less likely to be doing all the work...which prompts me to work a little harder. Once the stoker gets tired, going uphill becomes incredibly jerky; the rest of the time things are super smooth.
In other news, I figured out why I could not fit four of our new water bottles (which appeared to be the same size as the old water bottles) on the bike: I seem to have installed the down tube upside down (hence no clearance for the stoker's top bottle). I am a genius.
P.S. If you can't stand the taste of plastic in your water, Camelbak bottles are highly recommended.