Never mind, problem was with IDE 1.5, works with IDE 1.5.1 (though it didn't like my hardware/ folder).
So sketch is working now, and I can use EM-406A GPS pps to measure frequency of DUE clock/crystal and get measurements consistent with using an NTP host as frequency reference. The Sparkfun EM-406A operates at 5v, but specs and scope show TX and pps are at 2.8v so no level conversion needed. Frequency results and various sketches at