There's no way Nixon runs in 1964. After his losses in 1960 and 1962, he needed to recharge his political strength. It wasn't just Democratic strength that caused him to forgo a run. While Rockefeller no doubt would have run as he did, the same factors that caused him to lose to Goldwater, his divorce and quick remarriage to a much younger woman would cause problems. Goldwater won the nomination because he was the sole conservative candidate facing multiple moderate Republicans who divided the field (Lodge, Rockefeller, and Scranton). Much as the Republicans in 2012 had problems selecting an anti-Romney, in 1964 they had problems selecting an anti-Goldwater. There's nothing in your point of divergence that alters any of that.
Good point. However, if Nixon wins the election of governor of California in 1962 and somehow this causes Kennedy to survive, he may be up for the election of 1964.
I think if Nixon won in '62 and campaigned harder in '64 than he did in '60, I think he can narrowly beat Kennedy. He still has to pick a good running mate and figure out how to exploit Kennedy's weaknesses. Also, he has to perform well in the debates because he knows that they were his downfall four years earlier.
How about Nixon / Rockefeller vs. Kennedy / Johnson?