Chris,
I replaced the rubber snubbers in our rudder system this evening, shortened the tiller bar (since only about 3/16" of rubber was exposed between the tiller and the rudder arm), and realigned things. I can tell you that this boat is not modified in the sterns but the rudders are not square with each other and are canted with the hulls.
Alignment was a little frustrating. We tried taking measurements up high (staying as straight back as possible) and then down low. We couldn't get anything to come out right with accuracy better than 1/8". Frustrated, I slid the beach wheels forward of the daggerboards, dropped the boards in (had a friend put some weight on the bow) and sighted the rudders down the hulls using the daggerboards as a reference. We then came back and measured between the rudders just above the lower gudgeon and then back to where the rudder shape tapers down to the trailing edge. It measured perfect there, it looked right, so we set the screws.