Via Joe Carter, we get this AP report on John Kerry's extracurricular activities. His write-up in the 1966 Yale yearbook has him as a member of the Young Republicans during 1965-66.
Let's rewind the tape to the 1960s, shall we, and remember that the parties weren't as ideologically distinctive as they are today. There were plenty of liberal Republicans around in the mid-60s. Connecticut produced Lowell Weicker, who was their senator from 1971-1989, one of the last of the truly liberal Republicans; recall that in 1988, Joe Lieberman ran to his right in beating him, getting William F. Buckley's endorsement.
Down the road in New York, Jacob Javits was a liberal Republican, serving from 1957-81. In 1980, Al D'Amato beat him out for the Republican nomination, but Javits was still on the ballot as the Liberal Party nominee. In 1965, NY Mayor John Lindsey got elected on a Liberal-Republican fusion ticket. And, lest we forget, the original Rockefeller Republican, Nelson, was running the state from 1959-1973.
All these folks were significantly to the left of the modern RINOs and folks that a young Kerry might have been fans of. Given Kerry's upscale and cosmopolitan upbringing, it wouldn't have been too much of a stretch to see him as a limousine-liberal Republican, since northeastern liberal aristocrats tended to be Republicans back then.
It's only been in the last quarter-century or so that the parties have become more ideologically homogeneous. For instance, in the late 60s, Don Riegle was a liberal Republican congressman from Flint, not switching parties until 1973 and getting elected to the Senate as a Democrat in 1976; full disclosure, as a skull-fulla-mush fourteen-year-old, I (e-uuuu) worked on his primary campaign that year.
Thus, being a Republican in 1966 isn't something that Kerry need be ashamed of as a good liberal. Note that he was active all four years as a Liberal Party member; that should point to his true partisan loyalties.